UPDATE!!!! Car is running and driving, relativley fine!!!
Clutch, thermo, suspension, battery cable, etc. were all installed. I have been daily driving the car to and from work. It's I'd say 70% in good shape. Finally broke the clutch in. Still got a few problems
-roughness/loud/shaking - Focus_family looked at it and side it was passenger side mount. Ordered one of those
-VCT not working (worked before the clutch swap!)- my dad deleted 3 codes without writing them down, but that was over a month ago and they haven't come back. So think the solenoid is either disconnected? or needs to be dipped in brake cleaner or replaced. Focus_Family heard the intake manifold open up, but not VCT
-Idles high at startup - will idle between 1100-2200 in first few minutes of cold startup, then stays at 900-ish for the most part. Sometimes if I put it in neutral and roll to a stop the idle flucuates, but never too high
-Driver door is misaligned, hatch is misaligned, gas cap seems to open.close funny - think this has to do with the subframe being bent which shop told me, but I didn't follow up. Haven't got an alignment yet but it drives straight, but those items are misaligned. This issue worries me. Found rear subframes for like $120 locally. But dunno if that will fix the door and hatch misalignment. If I have to get frame straighetning so be it, for as much BS and $$ I put into this car to bring it back from the dead, i'm keeping it forever.
-sometimes there is a gassy/oily smell at startup, but always goes away. My MPG doesn't seem as high as I'd like but I guess at 70mph on the highway it's not gonna be prius like anyways
-lunchbox in exhaust is leaking water. Doesn't seem to be huge deal.
Thanks to everyone for all thier help!! I couldn't have done it without ya'll!!