I know that feeling! After I blew my first motor, I got a used long block and put it in. Tried to start it, and no joy. Turns out I had no spark because the new long block was out of an auto car, and the crank position sensor bracket (that bolts on behind the flywheel) is different from a manual.
Like you said, it sucks to have to drop the tranny right after getting everything back together.