So I drove it for the first time. She's definitely faster, and the supercharger whines like crazy with the intake on there. Best of all there was absolutely no KR, I need to test it when it's hotter out, but that is a good sign for now.

It did throw a P0300 code. Some googling shows its a misfire but I'm not really sure where to start with it. It has brand new autolite 104's gapped to .055 so I hope I could rule that out. I'm going to check the vacuum tomorrow, but it seemed to be around -17 to -20 when I checked it before the CEL came on.

Could it be related to the cat? When everything first got put back together fuel was pouring out the exhaust manifold because of two open injectors.