So you didn't run the new motor with the trans? Depending on what you changed, that potentially could explain the RPM spike and or the ET loss. You may not be missing something in the trans but very well could be missing something with the motor. You have changed a lot of things at 1 time.
Go back to the motor 1st. Recheck your timing, recheck your valves and check the plugs for a reading if you have not done so yet.