So I just rebuilt my 95 motor, it was running well except for when I would push the clutch in, the RPM's would drop and the car would run lean. It would happen so smoothly it seemed that it was electrical. I just had a relief valve stick so I had to pull my motor to replace the oil pump. The crank shaft has a pretty bad case of crank walk. I have another good crankshaft from a 95 so I'll replace it anyway. When I pulled my pan I noticed metallic dust in the oil. Then I looked at the rear facing thrust bearing and it was destroyed, worn down at least 1 mm. What would cause an issue like this. I'll check and see if 99 bearings were installed but this issue happening so quickly (just 800 miles) puzzles me.

Hopefully you can see the barb on the thrust bearing, it's a good 2-3mm of worn down metal

 

Probably the old bearing, or you had the right one and it was installed wrong.

 

Thrust bearing failures happen for numerous reasons:
Clearances out of spec-- leads to low oil pressure between the bearing and crank and incorrect operation when mashing the clutch
Low system oil pressure-- see above

Weird things I've seen on random cars:
Failure due to extended cranking while depressing a clutch on a setup with a really high clamping force
Botched transmission install that smashed the clutch/crankshaft into the thrust bearing
Weird pitting on the crankshaft thrust surface that caused premature wear
Someone installed an nb1 thrust bearing into an nb2 block that I bought... arg