binaryfail

The first line is there for reference. The second line is what you'll want to translate/edit, and that line will be filtered for insertion.

@Infernoplex
The codepage conversion warning probably means ahdprc is using cp936. You'll need to change it to 932 by editing the tool's source code and compile it again. The number shows up twice in the tool code.
Character's names in this game are prefixed with %LF instead of %LC, so ahdprc wasn't picking them up. Again, that'll require editing the tool and recompiling.
wpscrpt.cpp, line 50: change 'C' to 'F' wpscrpt.cpp, line 82: change "%LC" to "%LF" When the text is extracted, the character name will appear next to the line number within the script.

After the initial extraction from the ws2, the tool gives you a text file and a bin file. In most cases, you can leave the bin file alone. Here's a how-to if you want it.

The first one you describe might be this one.
The second one, I'm guessing, is this one.

The choices/branches involve addresses that are hardcoded in the script. Editing text in the script will often shift the address of where the script needs to jump to, so your error was likely caused by having the wrong address (or not updating it).
The first choice and a corresponding address for this game will look something like this. (image)
When it came to working with KoiRizo, I would initially recalculate the address (manually!) of each choice in their respective scripts. It wasn't too bad since there were relatively few choices to worry about. Later on, the calculations would be automated as a post-process, and knowing the location of each jump was required for that to work anyway. I should also point out that the H-scenes also involved jumps that behave based on whether the game is in normal story mode or scene replay mode, and the addresses in those also must be updated.

The choices/branches involve addresses that are hardcoded in the script. Editing text in the script will often shift the address of where the script needs to jump to, so your error was likely caused by having the wrong address (or not updating it).
The first choice and a corresponding address for this game will look something like this. (image)
When it came to working with KoiRizo, I would initially recalculate the address (manually!) of each choice in their respective scripts. It wasn't too bad since there were relatively few choices to worry about. Later on, the calculations would be automated as a post-process, and knowing the location of each jump was required for that to work anyway. I should also point out that the H-scenes also involved jumps that behave based on whether the game is in normal story mode or scene replay mode, and the addresses in those also must be updated.

In KoiRizo, the text for the choices are found at the end of the script where it branches off based on the selected option. example.

This version should fix the effects rendering in that scene. Download here.
Also added support for Shadows of Pygmalion, which uses the same engine with the same screen tearing issues.

Give this a try: download here.
It should help get rid of screen tearing on this game. This is currently experimental, so don't be surprised if it's a bit glitchy.

Those line breaks you're seeing originated from the game's script. ITH copied them as-is, but you can add a global filter in ITH to ignore the line breaks.
The filter feature is not available in ITHVNR, which means you must use ITH3 if you want to continue...
In your ITH folder, find and edit a file called ITH.xml Look for an XML tag that says <SingleCharFilter /> Replace it with this: <SingleCharFilter m000A="0" u000A="0" /> Save the xml file and start up ITH. The Options screen should should show 000A+ / 000A+ under the SJIS/Unicode columns. (see example here) Turn on the checkbox that says "Enable global filter" Click OK When you hook the game again, that should get rid of the line breaks when they're pasted into TA.
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For your other question: That address in your h-code is a relative address, so it needs to have a corresponding module name for ITH to find the exact address to hook into. That is usually the name of the game exe.
With that said, the corrected h-code would be: /HS8@220D0:DC3PP.exe
As a bonus, the h-code with the absolute address already calculated: /HS8@4220D0
That is the same hook that ITH3 should auto-detect already, so the above h-codes should not be necessary.

Those line breaks you're seeing originated from the game's script. ITH copied them as-is, but you can add a global filter in ITH to ignore the line breaks.
The filter feature is not available in ITHVNR, which means you must use ITH3 if you want to continue...
In your ITH folder, find and edit a file called ITH.xml Look for an XML tag that says <SingleCharFilter /> Replace it with this: <SingleCharFilter m000A="0" u000A="0" /> Save the xml file and start up ITH. The Options screen should should show 000A+ / 000A+ under the SJIS/Unicode columns. (see example here) Turn on the checkbox that says "Enable global filter" Click OK When you hook the game again, that should get rid of the line breaks when they're pasted into TA.
------------------------
For your other question: That address in your h-code is a relative address, so it needs to have a corresponding module name for ITH to find the exact address to hook into. That is usually the name of the game exe.
With that said, the corrected h-code would be: /HS8@220D0:DC3PP.exe
As a bonus, the h-code with the absolute address already calculated: /HS8@4220D0
That is the same hook that ITH3 should auto-detect already, so the above h-codes should not be necessary.

Try this h-code. One big caveat though is it applies to the latest version of Adobe Air (23.0.0.257) as of this time of writing. It will likely not work on older or newer versions.
/HQ-C:-14*A0@528CB0:Adobe AIR.dll edit: For some reason, the hook gets reset after the reading the first few screens in the game. Tested ITH3 and VNR, both are having that issue. I probably won't have more time to find out why this is happening.

I forgot to clarify, but an alternate exe will have to be made for each game/version. I'll do some testing and report back once I know more.

1. As long as everything else is working, those unknown devices shouldn't be a major issue.
2. The fix for Duel Savior might be applicable here too, but that remains to be seen.
4. You may consider changing the default Sans-serif font in Chrome to work around the iffy font rendering.
Go into Chrome's settings, Show advanced settings, find the "Web content" section and click "Customize fonts" -- for the Sans-serif font, choose a font that definitely handles Japanese such as Meiryo, MS UI Gothic, or Yu Gothic

There was a staff database on vntls.org but the site is now dead and hasn't been updated since 2013. Much of it can still be visited through the wayback machine: http://web.archive.org/web/20130810221613/http://vntls.org/staff/

Sort of late to this discussion, but the game can run on Win 8 or 10 with a bit of prodding. No virtual machine required at all.
Here is a modded exe that uses Wine's DirectDraw code : http://www.mediafire.com/download/9x4z0uwx2bz2gd4/ds_wineddraw.7z
I've actually been playing with it for the past week, so this seemed like a decent time to put this out here.

Playing with tablets+VNs isn't my usual combo, but I'll mention some things I've picked up. (I'm using a Nextbook Flexx with Windows 8, in case anyone asks.)
Instead of double-tapping to advance a line, see if a short swipe/drag will suffice for left-clicking. This also applies to menus and other game UI elements. Long-press and then swipe to make a right-click. Most games will bring up their system menu or hide the text window. The pinch gesture (just like zooming an image on a phone) emulates the scroll wheel, which should bring up the backlog for many games.  
I briefly tested Steins;Gate, Tokyo Babel (the demo at least), Hoshizora no Memoria, and Irotoridori no Sekai while writing this post, and they've been working fine with the methods I've described.

Playing with tablets+VNs isn't my usual combo, but I'll mention some things I've picked up. (I'm using a Nextbook Flexx with Windows 8, in case anyone asks.)
Instead of double-tapping to advance a line, see if a short swipe/drag will suffice for left-clicking. This also applies to menus and other game UI elements. Long-press and then swipe to make a right-click. Most games will bring up their system menu or hide the text window. The pinch gesture (just like zooming an image on a phone) emulates the scroll wheel, which should bring up the backlog for many games.  
I briefly tested Steins;Gate, Tokyo Babel (the demo at least), Hoshizora no Memoria, and Irotoridori no Sekai while writing this post, and they've been working fine with the methods I've described.

The folder you're looking for is in the local .wine folder (Notice the dot in front, it means the folder might be hidden.)

/home/YourName/.wine/drive_c/users/YourName/Local Settings/Application Data/Eushully/神採りアルケミーマイスター/SAVE
 

Getting a Japanese font:
Obtaining a copy of msgothic shouldn't be too difficult. If you have a Windows machine (Vista through Win8, or WinXP with Asian language support will have it), get it out from the "C:\Windows\Fonts" folder. If you can't find one, go here and click View Raw.
Once you have the file, move it to your home folder (because I'm assuming your terminal is opened there by default). The command here will copy it to wine's font folder. It is case-sensitive.
 
cp ~/msgothic.ttc ~/.wine/drive_c/windows/Fonts   Start the game by command line:
If you got the game dir from another system, that is okay. You placed the game folder on your desktop, so I'll guess from your screenshot. Doing a "cd" to that folder should look like this. You will need the quote marks in the command.
cd "Desktop/Kamidori Alchemy Meister" From there, use the appropriate command line to run wine. I'll use the same one I showed in my screenshot.
LC_ALL=ja_JP.utf-8 wine age   See if that works.

Sort of late to this discussion, but the game can run on Win 8 or 10 with a bit of prodding. No virtual machine required at all.
Here is a modded exe that uses Wine's DirectDraw code : http://www.mediafire.com/download/9x4z0uwx2bz2gd4/ds_wineddraw.7z
I've actually been playing with it for the past week, so this seemed like a decent time to put this out here.

So, no computer hacking experience but you got some computer whacking experience. Nice. (may they rest in p...ieces)
But really, it might be helpful to find a game and identify its engine first. That will help figure out what kind of tools are needed to get the data.

Yeah, that's basically it.
I currently don't know if a re-insertion tool is out there or not, so that will be something to think about if you're going to translate the scripts.

So, no computer hacking experience but you got some computer whacking experience. Nice. (may they rest in p...ieces)
But really, it might be helpful to find a game and identify its engine first. That will help figure out what kind of tools are needed to get the data.

The scripts are in Rio.arc -- are you able to upload it?