I don't know, but if they do, it would open up all kinds of options (assuming you could find a four-cylinder WD21 to get the rear axle from). If anyone on here knows about the gears it's probably @hawairish. You might also check Ratsun to see what those guys are running for axles and where they get their gears.
What's your target for cruising RPM at 70 with the TDI? If you can get anywhere close to the right ballpark with 4.3s, I'd be inclined to keep the stronger axle and avoid the scavenger hunt. Keep in mind though that fifth gear in the manual is about a 0.8:1 overdrive (the '95 manual says 0.862, the '97 says 0.811.) The autotragic's 4th gear is 0.694, so if you're not happy with your cruising RPM in overdrive with the slushbox, looks like you're gonna like it even less with the manual.
To find an LSD H233B, look for a big orange sticker on the back of the pumpkin that says LSD oil only. I don't know what those stickers were made of, but the one on my '95 outlived the frame.
Definitely get a build thread going when you start the TDI swap, I don't think I've seen that done on one of these yet.
Edit: This might help too, though it doesn't answer the question of whether R200 and C200 gears will interchange.
Edit again: Actually it does! Helps to actually read stuff, I guess.