5 spd, 95,000 mi

DTCs: 0300 random/multiple misfire
1133 O2S insufficient switching
0133 O2S slow response.
Surging idle when starting cold & will stall until it warms up.

Misfire causing the sensor issues?

Replaced plugs & boots, fuel filter, upstream O2 sensor. Ohmed coils (ok by Haynes specs), boots, housing and tested for trigger signal at IGN module, which read 7.5v - 8.5. Cleaned throttle body and IAC. Cleaning seemed to narrow the range of the surge but didn't fix the stalling.

Pondering the next step, I remembered we found a damaged wire in the coil harness. It was squished between the transformer body and the plastic frame that goes on top of the coils. There was a hunk out of it, but the wire wasn't exposed. I didn't have anything to replace it with, so I piggybacked insulation stripped from another wire. I couldn't find any sign of arcing, discoloration, etc anywhere nearby.

Could this be causing the misfire?

I think this is the primary & would've been more concerned if it was on the secondary. But - if it's grounding to the transformer body, I'd get an odd or weak spark-?

more detail here: http://www.automotiveforums.com/vbulletin/showpost.php?p=2893389&postcount=3

That may be you problem, I had a similar issue with my 96 2.4L 5spd. it turned out to be a crack in the plastic housing. I had a poor running situation, hesitation and missfire. After I replaced the housing
( about $60.00 @ Autozone) the car ran better, I did however have some other things going on, but the housing was a major part of the problem, My problem beganaroung 105,000 miles. 15,000mi. later the wholw hesitation issue was resolved with a ignition module change and fuel injector cleaning.
I hope this helps. Good luck.