Got the exhaust system all sorted out, was kinda expensive but it's done. Now I can focus on something other than the insane exhaust sound. Well, with the new exhaust (Stromung muffler from my old 4-cyl welded onto the 6-cyl mid-pipe using a Y-pipe) for some reason it's SO QUIET. It must have something to do with the smoothness of the inline-6, by the way it is INSANELY smooth, that the natural harmonics cause the engine to be easily muffled or something.
By comparison, If I were to accelerate with the 4-cyl and let off the pedal completely really fast, the car would lurch unless the ease off the pedal really slowly. With the inline-6 I can let off the gas and the car decellerates smoothly without lurching, I'm impressed.
Took the car to Autozone to have the codes read (the check engine light is on, no surprise), and theres 8 stored codes... Most of them seem to deal with emissions which is good and bad. Good in that they might have triggered when I basically ran the car without an exhaust and may be clearable now that there's an exhaust--Bad in that I need to get the emissions tested next month for my registration and a check engine light is a fail.
I also pinpointed where the shifter is hitting the driveshaft and its the selector rod making contact with the driveshaft balancer (?). I'll need to bend the selector rod to get it to fit without rubbing on anything, that should fix my shifting troubles also.
So a few more little things to fix but the swap seems to be pretty much done. I'll need to get a bigger rear diff soon before I get used to accelerating hard and blowing it up. The increased torque is noticeable for sure.