Reman engine running rough, multiple codes

[Rippin' Ranger]

I have a 2001 Ranger 3.0 V6 manual. I just finished putting in a remanufactured engine and it is running rough. Low idle, engine has a shudder to it. It drives but will die when coming to stop or push in on the clutch (engine going back to idle speed). It's throwing multiple codes. The global code is P0401 for the EGR system - which is all new. New tube, new sensor, new valve. Hoses are in good shape. Also P1000 OBD system readiness test not complete, P1124 Throttle position sensor A out of self test range, P1101 MAF sensor out of self test range, and P1127 Exhause temp out of range, O2 sensor tests not complete. Is there some kind of reset I need to do from putting the new engine in? Also my apologies if I'm posting this in the wrong spot, just let me know.

Also as I keep messing with it I've noticed that it starts easily when the engine is cold but as the engine warms up it seems to idle and run worse.

 

[superj]

I am not sure but it seems like just some loose wiring issue with all the codes. I dont know if there is some ecu reset. Since the battery was disconnected so long, it probably wiped everything already

 

[Rippin' Ranger]

I will go back through and check all the sensors/electrical connections. What about the camshaft position sensor? I have read some of those threads where people and rough running issues at warm temperatures with that. That thing is also a pain in the butt to adjust properly. But I'm not sure if it would cause all these codes to throw.

 

[superj]

I have no idea. I have read that too but my 3.0 has never given me any trouble and i still use it as a daily driver to work and back.

 

[Brain75]

If you haven't thrown sensors away yet, save em... "new is new, not necessarily good" is a mantra that started several years ago (I see posts by well respected very knowledgeable guys saying that in old threads)... turns out the aftermarket is crap times 10 now.
If you have the old, and knew they weren't throwing codes I would start replacing one by one and see if the codes go away.

 

[Rippin' Ranger]

I have the prior cam position sensor as well as the prior DPFE sensor. I didn't replace any of the others. I can try changing back.

 

[pentode]

Just a couple thoughts- the cam position sensor is in a mildly difficult position to work on but it's not that bad, and the only critical adjustment per se is that you're not off by a tooth (or more, but I don't think it would run at all off by two teeth). IIRC the computer can adapt the timing up to just about the width of one tooth -I did the math but it's been a few years - so there's no adjustment necessary beyond getting the initial installation right. Given that you didn't mention any CPS codes, my gut feeling is it's not that.
I'm thinking the TPS and MAF codes will probably lead you to the culprit. I'd start by looking around the wiring harness there as others have suggested. Good luck!

 

[SenorNoob]

Don't MAF and TPS run on 5V VREF? Check it?

 

[Rippin' Ranger]

I ran some live data off the code checker. The O2 sensors for banks 1 and 2 seem to be good, and the SFTF in range (approx -3% to +6%). The SFTF for B1 S2 (post cat) is at 99% but I read that is normal, given its after the cat? The MAF was also pulling proper lb/min. When I did the engine swap I put a new cam shaft synchronizer in. I think it may be off by 1-2 teeth. With the camshaft synchronizer in the position pictured below, that tooth that is peeking out under the sensor is the 7th tooth counterclockwise from the gap on the dampener (harmonic balancer). I read in one of the other threads on here that should be the 6th tooth, is that correct? The dampener is aftermarket and there are no TDC markings I can see on it or the pulley. I'm thinking it's not quite at TDC and that is throwing off the ECM. Thoughts before I pull the synchronizer out and try to get engine at TDC to re-implant it?

 

[pentode]

99% doesn't seem like a valid normal reading too me at all. Once you're over 25% you're usually into sensor/wiring/computer issues with OBD2 but I'll defer to the Ford techs here. Given that one bank is pretty much perfect, I wouldn't start suspecting timing issues. I'd be looking at wiring and sensors first.
I think it would struggle to run off by one tooth (on the cam sensor) and two I doubt it would run at all. I think you're off by 25-30 degrees at that point.

 

[pjtoledo]

you can stick a long thin screwdriver in plug hole # 1 and feel the piston hitting TDC.