If they didn't replace the sway bar bushings I'm thinking those could be the culprit. They clunk when both wheels drop. Any auto parts store should have the pair for $10ish, it's a 20 minute job. Just need an 18mm socket. Don't need to jack it up or anything. I'd start there, I think most KJ clunking noises come from there. It's rare to have bad lower control arms on these.
For the grinding noise, is it a metal on metal grind or more like an electronic buzz? The buzz is completely normal.
For the window regulator, typical KJ issue. Easy fix.
For the suspension, OME/Bilstein is much much much better than anything OEM or from Rockauto. It seriously saved me from trading in the KJ. The ride is so much better. But Monroe will be like OEM.
I think I got everything...did I miss anything? LOL! Wish you weren't having these issues!
So I am at the dealership. They informed me that the sway bar bushings were replaced when the other work I referenced above was done. In this case do you think the suspension is causing the clunking? Also just wanted to note that when I got here the squeaking I referenced that was coming from the engine actually seems to be coming from the transmission area, they said they think it's the torque converter, any ideas? Again, thank you for all your help!!