Carefully inspect the suspension mounts, and especially the top rear shock absorber mounts for rust. I've had two 99's let loose there. One was easy to fix, the other was very hard and needed a bunch of metal welded in.

They also have rust troubles at the bottom of the side doors and the bottom of the B pillars, but these won't cause trouble while driving.

The 5-speed manual is based on their venerable and robust 4-speed used in the 99 and shares a lot of parts. However, when I say "robust" it is in comparison to the older V4's where the transmission was a very weak spot. The engine is very easy to work on except for the water pump which is located under the intake manifold and pressed into the block.

Is that still a K-jetronic (CIS) system?