Alright, big update. Due to time restraints, I didn't get a new tranny to engine shim (the one that was all tore up). We tried looking for one locally but couldn't source one and didn't want to wait for on to come in the mail. We decided to beat the hell out of that one and make it work.
After getting everything back in, we were trying to bolt the flexplate on but we were off 1/4" on one hole no matter where we lined the bolts up. That's when I did some research and found out 93-95 flexplates are different than 96-98! We didn't want to take the tranny out again so we said screw it and egged the hole out more with a plasma cutter. That worked, it bolted up.
TIME TO START IT! We fired her up only to have our ear drums ripped apart by the loudest metal on metal sound ever. It turns out, that shim was bent so bad the flex plate bolts were hitting it worse than before. We crawled under there with something to pry with and after a good 10 minutes of fiddling with it we got the noise to a minimum. That's when we decided we have to buy a new shim
The reason we were in a hurry was because my dad had to leave for a business trip and wouldn't be back for a week. I ordered the parts and they came in yesterday, the day he came back. We got the tranny pulled and replaced the shim AND flexplate with new ones and everything is kosher now. Ended up getting the whole thing done in about 4 hours.
So in all, we replaced the flexplate, tranny shim, flexplate bolts, transmission, rear main seal, both oil pan gaskets, tranny filter, tranny fluid, fuel pump, spark plugs, plug wires, distributor cap and rotor.
Total investment including ZJ: ~$850 and a good 12 hours of work.
Now that's it driving again, next thing I'd like to get is a 3" BB or F>R spring swap with 31x10.5 tires.