I'm pretty much right where you are in parts for my swap. I did the 5.3 from BDTurnkey. It sat a few months at my house after I got it from Bryan. While my project was a full frame off CJ7, I got the engine early for fit up and fab. When I had it in the frame, I rigged up some switches for power, horn button for ignition, engine started first time and ran perfectly. The Novak mounts were exactly right, mine had six bolt holes on each mount and suggested to weld the top lip to the frame. Very well built and beefy. I also bought the ECM mount from Novak, highly recommend this. It does a great job for mounting the 'puter. I decided on the Level 2 TH350 trans. Arrived with everything right to bolt to my D300 TC. Also had the dustcover and detent cable. I changed the dip stick to a Lokar unit. The Sanderson headers are like yours, very well made, fit perfectly to miss the frame and was easy to build exhaust. I used shorty cat converters from Magnaflow. Mine are true duals all the way out. I centered the fuel tank to have equal room on both sides.
I bought a Jeep Air unit for A/C, they have the right adapters for your A/C compressor if you decide to go that way. I am going to use a Viair elec for my onboard air supply.
Close to complete with mine, have driven around the yard. I need a longer throttle cable and need to build a bracket for the detent cable. Using a new Painless kit and adapting to the 5.3 wiring. I think I'll be done about Mar or Apr. If I can offer any experienced based info, feel free to contact me.