FTBR IRS Bushing Locations
There are pictures here. Also a good source for suspension parts. The bushings on the diff would be the next likely source of the clunk.
I know when you switch to an after market throttle body you have to set the tps voltage to .98, do you have to do that when putting the factory one back in and have you done that? Also could you unplug the idle air control to see if the idle drops or stalls to see if the car in commanding it...
May want to check if your radiator isn’t blocked somewhere. When the car is hot the radiator should be pretty hot all over as well. If it has cold spots than it may not be working properly anymore.
I have seen people on here saying you need to lube up the cable, even brand new ones, and that helps considerably. My factory cable with spec clutch is pretty soft, but chattery like mentioned above.
It has been many years since I replaced my abs module with a used one off eBay due to the original leaking brake fluid. I don’t remember doing anything special besides plugging it in, reconnecting the plumbing, and bleeding the brakes. No abs light and I just drove it after that. Not sure...
Another thing to consider is that back in the day I insured my beater as my primary car with just liability and my mustang as secondary with full coverage and insurance was cheaper than just having it on the mustang.