I think I figured it out. When I swapped the transmission, there was one ground on the transmission toward the front of the car under the front manifold/crossover pipe connection that I apparently did not tighten down enough. I guess the connection was flaky enough to cause electrical issues, which would explain why my misfire was intermittent. Once I got the nut holding the grounding wires tightened down properly, I had zero misfiring. Stupid simple fix.