TonyQ97ZJ4

To start, I bought this '97 Grand Cherokee Lared 4.0 2WD with 42RE Transmission back in 2009 while at Ft Knox, Kentucky with 192K Miles and now has 240K Miles. Drove it back and forth from Kentucky to Washington State 3 times and other long trips to Yellowstone Park, Seattle and other distant places. Only issues were computer, coil pack, fuel sender unit and doing normal maintenance. Just back in December of 2017 had issue with the Flexplate bolts backing out and being sheared off. Replaced the Flexplate as cracks were found. Replaced Torque converter since bolts were broken off in it. Rebuilt the Transmission with new Clutches and Steels; Accumulator Springs, Gaskets, O-Rings and Seals; Valve Body Springs, Pistons, Solenoids. Everything was put back together and fired it over and went on a test drive. Everything was working perfect in town and then on the highway, something happened as I lost power and the engine started to sputter. Got it home and noticed a rapping/tapping sound from the front. Also Engine light was on and a Code P1391 was present. Changed the CPS, still same code and noise. Researched and found out that it was possibly the Timing Set was worn out. Which it was. Since I was pulling the Timing Set Cover off, I went ahead and removed the Oil Pan and change the Oil Pump to a High Volume Pump and Rear Main Seal. Made sure all of the Marks matched up on the Timing Set and removed it. Put on New Set and keeping marks perfectly aligned . Put everything back together. Started it up and Engine ran like something awful. I verified timing marks and everything. Cylinder #1 at TDC with notch on the Harmonic Balancer lined up with the Timing Bar at 0 degrees. Then I thought since the Timing Set was original, why not the Distributor? So removed the Distributor Cap and Noticed the Rotor was pointing at the #5 position, Put the Cap back on and lined up the #1 and the #6 posts with a yard stick and placed a mark on the fuse block cover to help lining up the new Distributor. Put in new Distributor and made sure the Rotor would point to the correct spot at #1 TDC. Put everything back to together, cleared codes and started up. Engine started up but was running still running rough, with RPMs going between 1200 down to 300.and the same code P1391 came back. So researched more and finally decided to change the CPS again. It was a Duralast and swapped it with a BWD. Cleared codes and attempted to start. It took a while, but it finally started up and it idled fine for a bit, but then the idle would fluctuate between 600 and 850. Pressing on the gas would result in misfires. IAC and TPS have also been changed out. Still the same. Just wondering what else I can do now. Was thinking that I may move the distributor either one tooth ahead or one behind?

97grand4.0

1391 could be either cam or crank sensor. BOTH THESE PARTS MUST BE MOPAR. DURALAST WILL NOT WORK. Aftermarket parts here will not work.
Also, the distributor must be in correctly. There are sections here on how to do that. I had some fits with my CAM sensor. It's an easy swap unlike the cam sensor.