Looking back on an older project (honestly hoping to finish up with it, but no luck on that front), I've made a little more progress with the ever-faulty Alice in Kaeru nyo Land code. Like a caveman beating a shotgun against a rock, I've eventually learned some should have been obvious features in ALDExplorer that allowed me to stick the game's code into one file. This has fixed the errors with the DLC's TALK##.ADV files. I've also got enough of a grasp on System 3.5's hellish array and loop code to suggest that the MINE##.ADV files, which looked to have errors similar to the TALK files, are actually correct. Go figure.
The biggest problem now are external file reference errors. Good results here! Combining the files fixed several of the errors. It didn't fix all of them, but this showed me that this is actually Alicesoft's own fault: it seems they left the code open for even more DLC than we actually got - since the code had no way of checking how many files there were dynamically - leaving slots for a total of 20 expansion files when we only got six (two that came with the game). Long story short, once I point everything in the right direction and remove the open slots, this should work. If it weren't for an unrelated error tied up in System 3.5's hellish loop code, I might have even tried it by now! I have no idea what's wrong with the loop code, but other than that, prospect: hopeful?
Another potential problem is that, since Sys3Decompiler relies on not only a single ALD file, but a single pre-existing ALD file, I'm putting a lot of weight on my caveman-meets-ALDExplorer hack fix. If it's not enough for Sys3Decompiler, I'm not sure what I'm going to do to make the code go back together.
In the midst of my troubles I went to check on that other lingering 3.5 decompile problem, Persiom, and re-discovered that its problems were all external file reference errors, too. Except Persion doesn't use multiple code files! After some investigation, and to the disappointment of my Cut Content project, it seems Persiom's devs removed its debug code file (file 3, added very early into the project) after the game went gold! The only remaining references to the file are the original debug access menu, and various array-related error reports (which ironically might cause the game to crash in this modified form - guess they're really confident in their product!). While this is disappointing (I'm holding out hope that the file was just renamed or something, cross your fingers), the problem code is easily removed and I should be able to get a decompile ready without much trouble... if it weren't for another fucking loop error! With this happening two games in a row, one wonders if Sys3Decompiler is at fault, but I guess we'll see.
I wish I was a little closer to actual results but all considering this is good progress.
EDIT: I've nearly got the Alice Nyo fix. The code is probably intact, I'm able to update it and translate it, the game runs to a point, the only remaining problem is the DLC. It's a weird one: for some reason, Sys3Decompiler itself is mis-saving the DLC SCO files so that they refer to the wrong code file, which I didn't even know was something they could do. This causes a crash during boot. I've tried manually correcting them with ALDExplorer but it's not working, and it's a problem I should probably address in the decompiler anyways or it'll just reoccur. With luck this'll be the last of the problems.