VW 01M sutomatic transmissions were garbage. For more than 5 yrs now, though, most have been DSG transmissions rather than traditional automatics. They aren't spectacular, but haven't been the worst things on earth. The DMF's have been known to grenade, though. The manuals are great, though, and aren't bad to work on. There was a time when the DMF's on some of the manuals were causing problems, but much less now.
You can get LR short blocks for anything prior to 2003 for about $4k or less. Used engines go for much less around here. I've seen plenty for cheap, and got a 4.0 that had a top end rebuild prior to being wrecked for about $250.00 a while back. The problem with any of those trucks is that the general electronic and other assorted problems have the truck worth less than $5k and the fuel economy is going to be about 12-14 mpg. There aren't too many people who want to sink that kind of money into something that is that bad on gas and is subject to many other expensive repairs, especially when 95% never get off road. The newer models, well now that's just another very expensive story altogether.