chrysler tech here and the fireing order is not 123456. the pics above posted by crazy are what you need to look for on your's. the 3.9 is a v8 that literally is missing two cyls and they wer all the same inside minus a few minor changes when the went from la the magnum engines. also #1 should be marked on your cap if it's a mopar cap. if not pull the plug from number one (left front) get it on compression stroke (valves closed at tdc) and where ever your rotor points is number one. it's worth the ten mins it take to double check the fireing order. when it's running lower rpms it would have issues that either smooth out or become less notecible at highr rpms. also check all of your engine and body grounds while your at it. few extra mins but on occasion i have found my issues that way. wether i notice a wire frayed while im doing it or i find an actuall ground issue. example older 4.0 fords the crank sensor wire went down the front of the motor and snaked behind the belt and pulleys. customer brought it to us missing and stalling with no codes. when i looked at my grounds i noticed copper showing through crank wires and it was shorting basically crashing the pcm. start with the basics and keep it simple.

 

btw it's 12 foot pounds not 2 :P

 

I took the Bat cable off and let it set a few days so the computer could reset and now I get code 11. I going to try another CPS on it and that will determine if the timing chain needs replacing. Washed off the intake and found the firing order and you were right It's 165432. The chilton manual is wrong, and so was my friend.

 

Ya the IAC was in the way of the 1.

 

Just to add to the issue:

You mentioned your rotor being off by rotating the crankshaft. If it is 15 or so degree's off then you may want to look at your timing chain, or your distributor seeing as they are so different.

 

Checked it out today and determined it is the Chain. Checked my service records and discovered this chain has 157,000 miles on it. Time for a chain. :-) Thanks for everyone's help.

 

Update. Finally checked it out a few days ago and it was the timing chain. Put one in and it runs great. No more Back fire [friss] :] Thanks everyone for yor help.

 

i just pointed that out crazy because i know a few gullible ppl that would attemp that low torque and trash it lol. i just find in this buissiness it's best to cya (cover your a$$)