I really appreciate all the help - thanks very much. I am in the process of leveling everything right now. I have the car leveled and the subframe loose. I am going to run and get a dowel this afternoon to make sure it is plumb. The kit came with 6 bushings. 2 of the larger diameter bushings were thin and two were thick. The smaller diameter ones that go with the rad support (I am assuming) are the same thickness as the thin set from the larger diameter. I have the large diameter thin ones in the back of the subframe, the thick ones in the front, and the small diameter thins in the core support. I will post the results after I level everything.
To give some background as I have been working on this for months now:
I was pretty sure I put the bushings in the right way as I have the assembly manual. I put the bushings in the way I have them now the first time and the issue was obvious when I laid the first fender on the car. So I went through several iterations of pulling the subframe, changing the bushings around, switching the order in which I tightened, etc. I tried about everything I could think of. The holes all line up fine, so I didn't think the subframe was bent. However, I did notice that the subframe has had one of those mount repair kits welded in. Whomever put the repair kit in cut out the top of the rear subframe and welded the 1/4" plate in. They welded the firewall mount repair underneath the existing subframe mount - so it seems like the rear subframe mounts are ~ 1/8" higher than they would be stock, and then the firewall mounts would be the same - but I don't have another subframe to compare it to. My thinking was that this would pull the rear of the subframe down a little bit and cause the subframe to sit tilted. Run that small tilt all the way out to where the radiator support is and it might be the problem as it would sit higher. So I had a friend of mine who is a machinist make me some spacers 1/4", 3/8", and 1/2" thick that I could put on top of the firewall bushings. The thicker the spacer, the better the gap gets. With the 1/2" spacers in, the gap is the best, but it looks like I'd need about 3/4" spacers to get it even. Something about that just didn't seem right to me. It didn't seem like that little difference would justify needing 3/4" more spacing a couple feet forward where the firewall mounts hook up. I even dusted off the geometry skills to try and figure it out.
So thanks again for the help - I just want to make sure I find out what the problem really is, as fixing it later would be much more work.