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Okay, our early '99 Powerstroke just developed this problem. It was running just fine all of a sudden the motor developed a major miss problem, sounded like it was running on a couple cylinders. Now (after cranking and cranking) it started and now it sounds like one of the cylinders is still missing. Also when idling and missing, the O/D light on the shifter lever will flash on and off. Any help would be appreciated.
My first guess would be the UVCH. You can try unplugging one side at a time to see if it makes it any worse or not. If you have one side that doesn't change the way it runs start by pulling that cover.
I don’t know how different the diesel is from the gas burners but our 99 F150 had similar electrical problems and I replaced the GEM that is on the back of the under dash fuse panel and it took care of our window and interior light issues. Also our odometer worked intermittently so had to remove the whole cluster and re solder the power lead to the odometer...sounds like you could have multiple things happening here...
F350-6 has good advice for you here. I don't think the blinking O/D light is related, but it would be helpful to get the codes and see what that issue is. OBDII Tools link in my signature will set you up to read them if you need a scanner.
You can set up your signature where you can include your truck info, by clicking on "User CP" near the top of the forum page, then "Edit Signature" on the left.
My first thought for long cranking is oil related. Is the oil full? Sounds like a dumb question, but my early 99 did something very similar when it blew an injector o-ring and you'll lose a gallon of oil in no time.
I have a similar problem with my '99 7.3L. Just started running rough and low power. Starts ok, no smoke.
Fuel filter light is not on ( is there one on 99's like my 92? ) Has fuel. Oil level is correct and is clean.
No CEI's afaik.