Today I swapped #3 Fuel Injector with #2 to see if the misfire would follow the injector. This is where it gets interesting. After reinstalling the fuel rail I was getting misfires on Cylinder #3 (the original issue), Cylinder #5, and Cylinder #6. I could hear a hissing sound like a vacuum leak too. I took it for a test drive while I monitored the misfires and the misfires would stop when the rpms were above about 1,000. I removed the fuel rail again and realized the lower injector O-rings weren't seated correctly on #5 and #6 but #3 looked fine. I reseated the O-rings, reinstalled the fuel rail and I was back to just #3 misfires. When I switched #2 & #3 injectors the lower O-rings stayed with the cylinder so this got me thinking maybe it is just the O-ring. I took the fuel rail off again and removed and inspected the #3 lower O-Ring. It appeared to be fine and I couldn't see obvious deformation. I had a set of spare upper O-rings which are just a little bigger, so I tried that and the misfires got much more frequent. I took it for a test drive, and again the misfires only happen at lower rpms. The Jeep seems to drive fine.
I ordered a set of injector seals (2 O-rings) for one injector from Extreme Terrain. They'll arrive next week but I'll be out of town all next week so it will be a while before I post another update.
If anyone has any other ideas on what to try, please share.