The Mk3 and Mk4 transmissions should have the same mounting flanges if they're MT.
You're suggesting that because the carrier is from the Mk3 that there's going to be a problem with the axles? I would probably say that's not going to be an issue.
You should look for complete axle shafts from Mk3, B3 or B4 vehicles, 4 cylinder with MT. That's a very broad scope but that will get you what you need.
It might also depend on what model the control arms you're using came from but I would tend believe they will work.
Yes, the CV joints are at either end of the axle shaft. When talking about the complete shaft I say axle assembly.
Brand new axles - those can be mixed bag if they aren't patterned after the originals. I would tend to hunt down OE axle shafts and then see about finding good CV joints I can repack and reboot so I can make complete assemblies. Like I said the passenger axle assembly on the Mk3 is hollow on TDI cars, and possibly even on the 2.0 ABA 4cyl cars too.
Steve