Ok looking for some advice. 

Ok, so I bought a 99 dodge several months ago. The engine has been swapped out for an 02 engine and computer. The internal tone wheel had been retrofitted to the front of the balancer. 

For several months the truck had a p1690 code. I did all the checks on this page and everything checked out fine. 
 I finally got it to go away by rotating the tone wheel 180 degrees on the balancer and the code is no more. 

Worked good for about an hour, than I got a code for p0216 accompanied by the dead pedal. 

 

Truck has always had a lopey inconsistent miss at idle. Even after the p1690 code was fixed. 

 

I can Hotwire the pump and it idles great nice and smooth with no miss. 

 

Looking for a direction to go.

Ok so for an update to make things even more difficult. I can unplug the crank sensor on the front of the engine and it idles a lot better and and the p0216 code goes away and gets replaced with p0336.