Rear sub-frame issue is large. There was actually a class action lawsuit regarding it. Try to find out if it has been repaired. If not there’s a high likelihood there are tears in the sub-frame structure.
Personally, I’d choose a 2000 model over a 1999. I realize beggars can’t be choosers. The 2000 got the upgraded steptronic five speed transmission. Assuming you’re looking at an automatic. It also got a new and improved Dynamic Stability Control system.
One additional item that comes to mind is power window regulators. The E46 is known for failing regulators.
Be sure to check out
www.e46fanatics.com. There’s more information there than you’ll be able to absorb.
https://www.e46fanatics.com/threads/...guide.1007722/
Good luck.