It's pretty common with most Jeeps to have variances in the bracketry and flashings. Each one off the assembly line have subtle differences. I'd recommend clearance the frame bracket so the bushing is free and eliminate distortion. Spray on a little paint after to control the rust.
30 years of desert racing and rock crawling. I'm not surprised at anything these days. I've watched the Sierra Club do more damage in an hour to a trail then a full race field of 1000hp trophy trucks.
I've lost a countless amount of the electronics in these swaybars. We just end up running the EVO MFG No Limits manual disconnect and a Tazer Mini to turn it off. NO LIMITS MANUAL RUBICON SWAYBAR DISCONNECT JK/JL/JT | EVO Manufacturing (evomfg.com)
Personally, I'd install the lift now. This way you can get a little break-in time on the kit.
Ive been going to EJS over 20 years. It's a great event. You'll enjoy it.
Now if you are looking for the best on and offroad suspension system for your JT, Id give this one a serious look 3.0"...
Side Note: RK does recommend bumping the rear springs up 1" for heavier JT's.
If building an "overland style" or heavily up-fitted build in the back, we recommend upsizing 1” in coil lift height for the rear.
I've chased a handful of noises similar to this. Ended up the rear most hydraulic cab mount on the race JT as well as the shop truck. No problem with them, they just made a slight knocking sound.