The engine seems to idle normal and doesn't seem to act up below 3k rpms, but once it's up there it completely bogs down and I can't seem to accelerate without switching gears. I'm not completely sure if this has anything to do with my issue, but I wrapped the turbo with a heat shield that may have covered the wastegate actuator arm. After removing the heat shield, the problem was still present.

It turns out that it was simply beyond the point of needing a tune up. For some unknown reason my mechanic did not replace the spark plug wires, distributor cap, or rotor during my swap. I replaced all of those yesterday and now it's running better than ever.