I flushed the transmission with synthetic fluid. While I was at it, flushed coolant and fuel system. On the way back the car started running poorly. Stumble, lack of acceleration, tachometer needle is jumping up and down quickly (engines don't speed up or slow down that fast). I am thinking Crankshaft position sensor?

The car now has a hard time starting, unless I give it a little gas. But it starts, oddly enough.

 

I suspect you have wet the coils and spark plug boots. Take the cover off the coils and check that they are dry. Then check the CKPS connector for water.

 

I will check that, thanks. I would be very surprised if I got them wet. I suspect that something attached to the engine is misbehaving due to heat. The car sat idling for a very long time,during all the flushes. I was trying to chase out accidental stumble that happens infrequently, which is why I did the trans flush.

Usually it happens like this: I drive to work, spend about 30 minutes on the freeway the car runs fine. I get off the freeway and it stumbles and stalls either on the first or on the second light. It always restarts, though.

The stalls used to be much worse, but after I replaced fuel filter and TPS and caught up on a bunch of other maintenance they became a lot less frequent. I suspect either crank sensor or coils getting hot and misbehaving.

It also could be a flaky fuel pump. I only get a the generic misfire codes "mixture too lean" but I don't get cylinder-specific misfires. Which makes me less inclined to suspect coils an more inclined to suspect something that affects the entire engine. I could be wrong, my car is a 95 and the firmware is half-baked in these. I will swap in a spare ECM before I spend money on coils, just to see if the later ones are better at detecting misfires. I have IDS, so resetting should not be a problem.