A few thoughts - 1) Gutted cat has lowered the back pressure, thus the O2 sensor may not be reading correctly. 2) Check the fuel pressure to see if the regulator is working right. Who "rebuilt" the throttle body? I would assume if it was rebuilt, they would have replaced the TPS, the pressure regulator, and the injector. Along this same thought, check the TPS to make sure it's reading right. Should read between 4.6-4.7V. 3) Check the Wide Open Throttle switch. This richens the mixture at WOT. 4) Check the MAT. 5) Make sure the injector isn't leaking. I would assume this also would lead to flooding when starting, so probably not a problem.
You can also search google for Jeep Wrangler D1 diagnostic to find some info from the FSM. Look for a URL that ends in .fr. Should be the first hit.