Hrm. Well, I'm just sorry that I wasn't able to help you actually solve the problem. It's just not my area of expertise at all - I'm a novice with internal computer hardware, and in some respects this is on a higher level.
The one thing I will say is that it's highly unlikely that someone else tried to pull a battery switch before you. Most people wouldn't dream of attempting it, particularly without a guide like Master Kirby's. So the internal workings were probably unaltered when you got it, aside from the battery being out of power. (If you're still unsure, it may be worthwhile to try to find a picture of an open cartridge online for reference.)
Other than that, I'm afraid there's not much more I can offer. Master Kirby still drops by occasionally, so maybe you can catch him then. Or you can try to contact him through his website, or something. He has a lot more technical know-how than the rest of us; he's the one who started this whole thing, after all! So he may be able to offer some advanced insight. Or maybe you'll be able to figure out some alternative solution to your dilemma. However you proceed, though, I wish you the best of luck!