I had all kinds of issues when I tried the injector swap just like you are. My Jeep ran like shit and kept dying after a really low idle. There was also lots of carbon in the exhaust.
Not only that, but my 1st injector stopped working correctly and I had to run on 3 cylinders for a few months. The reason that happened was because I had one of the plastic connectors crack into 3 peices, so I went to the local pick-n-pull yard and took 3 connectors off of a cherokee and just put one on (took old one off and put wires in new one).
Now, my injectors were bad and that's why my Jeep sounded terrible and died after starting it so I swapped the old ones back in and took the injectors back, suprisingly they gave me my cash back and the Jeep ran fine again.
I recently ordered a set of 4 Gen 2 19lbs. injectors that were refurbed and I'm hoping I'll have better luck this time.