I been working on an 06 xterra with a 4.0. Long story behind this one. This friend bought this one with the trans removed and missing all the parts to do the transmission replacement. We found a transmission and when I was attempting to installed this replacement I found lots of rust on the flywheel flex plate and starter drive. Too much actually. This thing sat up for maybe 3 to 5 years at the repair shop that told him no transmission was available.I sandblasted these parts and a light coat of cold galvanize. I am 95% sure I put the flex plate back the way it came off.The reluctor looked ok. Got the car running. I noticed service engine light on scanned and code for crank sensor. Replaced sensor but still engine miss on one cylinder. Replaced plugs that were fouled with raw fuel.. At this point I do not recall if it hit on all 6 or not. But I do know at times it did run fine. A few days went by and this thing lost power at which time I found one cat plugged. Removed the cat and cleaned out the inside. Power returned but miss on cylinder 1. The owner drove it anyway and clogged the other cats. Replaced all cats with aftermarket. Took me a day and a half with these junk parts. They did not fit properly, had to heat and bend to fit plus remove shields from old cats and use clamps to install on new cats. Removed the plenum again and replaced an injector and coil. Ran fine and then after a short while started missing on cylinder 5. Replaced coil and it hit on that cylinder for a while but then came up with missfire on cylinder 2. Checked spark on that cylinder and no spark. Checked power and ground to that coil and I have it. I have not put my scope on the trigger wire yet but probably pointless. I believe not getting signal to fire that coil pack. Now i am wondering what the hell is going on with this missfire jumping cylinders. I am wondering if I go the flex plate out of sync. I looked at the old marks and I thought I put it on correctly but may have not been on right from the the beginning. Since the shop owner stole parts off this car during the time it sat there. Also when I sandblasted the reluctor did i mess it up? Since Mitchells states do not scratch and bend the reluctor or magnetise it. I thing the rust would be worse that the sandblast job I did. I am an ex auto tech but this one is making me pull my hair out. Please help.

It would be throwing crank codes instantaneously if the reluctor was mis-located, so that's not the issue. Have you checked ground integrity on the electrical system? Sure sounds like a ground gremlin!

post6817410.html?hilit=ground#p6817410

Only ground issue I see is the ground on the exhaust system is broken off. I do not think that is the problem. I will will check grounds again though.

The ground on the exhaust is just for the rear O2's, that definitely won't be your issue.

Ok problem solved for now. I was chasing my tail. I had multiple part failures. Had 2 bad coils. The one I was using to test with was bad too. Through me for a loop. Then I remembered that the auto shop owner was using parts off this car and putting bad ones back on it. Thanks for help.