Misfire problems (not your average misfire.)
 

Sunday I changed out my water pump, go to take it on the test drive and all of a sudden start having misfires. Throwing codes for multiple on 1 and 6. I changed the plugs, it got a little better but you can still hear the misfire.

So I for the hell of it did a compression check, all cylinders between 140 and 130, no issues there. Swapped in a brand new coil pack (01 gotta love that coil), problem is still there. Its not so much that its throwing the code, but its a rough idle that you can tell the miss is there. Normal driving is perfectly fine. It also seems that the miss is 100x noticable when the engine is at normal temp (200). I though about it maybe being heatsoak, but that affects mostly the middle cylinders.

The injectors are 784s that were rebuilt and cleaned a couple of months ago, and while it still may be two of them thats bad, I find it hard to believe. Today I moved around the injectors a bit to see if the misfires follow or stay put. Because all of this came out of nowhere it makes me feel like its an electrical issue, that i bumped something while doing the water pump. Next step is to get a noid light tester and see if the injector wiring is good. Other then injector wiring I can't seem to figure out what it maybe. Would love to hear some feedback on this, it kills me that all of a sudden its running so nasty and that I am having such a hard time figuring out what it is doing it.

Helped someone out a few years back that had the same issues after he changed his water pump,his problem was someone mis boxed the pump, the impeller was the wrong rotation for his application even though the parts store swore it was correct! BTW his seemed like it was running at normal temp but after shooting the head with a IR temp gun the front and back cyl.s were 40 degrees hotter yet the gauge read 210.
Only things he had done was all new hoses,thermostat and water pump,before he asked me to give him a hand he had swapped inj.s put in new plugs,changed the computer and a bunch of other stuff that I can`t recall at the moment.
He still had his old pump and I asked him if he had compared both of them before he installed the new one he said yes and they were the same, we pulled the new pump and low and behold the impeller was wrong!!
I would have thought that this would have caused it to overheat but it did not! Installed the correct pump and no more misfire, but it did blow a head gasket after about 5,000 miles (Gasket was blown at #6 near the rear of the cyl.)
BTW his ran o.k. til it got up to temp ,if yours is missing when cold I doubt if this is your problem
It`s a long shot but might be worth looking into since all you changed was the pump. Good Luck!

Just thinking about your problem some more did you try a new CPS?
Since the coil pack type ign fires two cyl.s at the same time, cyl 1-6 ,cyl 2-5, cyl 3-4. I can`t figure out why it would just cause a problem on 1and 6 though,and what changing the water pump would have to do with it. Maybe another long shot but worth a try.

Also thought about the Cam sensor but that only does the fuel inj. sync

Gotta chase those codes that you are getting. The OBD II system in your 01 is pretty good at pointing you in the right direction.

1. Did the engine overheat recently? Are you using any coolant? The 0331 cylinder head in your 01 can crack, and cracks can lead to misfires. The #1 symptom of a cracked 0331 head is "unexplained coolant loss".

2. What brand plugs are you using? There have been a number of reported incidents now with Bosch plugs. Changing the plug mfg. resolved those misfires. I use the NGK V-power copper plug gapped to .035 in the 01.

I did look at the impellers and they looked like the right application, it matched the stock one I took off. Cps is 2 or 3 years old, don't think thats the issue. I took the number 1 and 6 injectors out, and things got a little better. It was fine for a day and now back to having that rough idle and a lovely "put put put" sound from the exhaust.

I am going to try to swap back to stock injectors to see if that helps any. Im upset that I thought I had fixed it and it had seemed like it was good untill I drove to work this morning and it was rough again.

This is a reman engine with only 10,000 miles on it, a cracked head is unlikely, and the compression test would have showed something if that was the case. I am not losing any coolant. I have also never overheated the engine. I stick with the cheap champion coppers, and I make sure they are all gapped to .35 myself before I put them in.

I have also not been able to get it to throw another misfire code again. But idle and exhaust sound is not right. Previous had been getting codes for small and large evap leak, but thats been there for years and the only way Im going to find that is to smoke it, the whole system has been checked. I had a code for main cat efficancy below threshold bank 2 that was showing up, not sure if the o2 sensor is crapped out, or the cat is. Something im going to start looking into is the o2 sensors.