Guess I screwed the pooch on this one. Guess I'll have to pull the engine and tranny out again.
No, you can leave it in. It will fill just fine. It is just a good practice to add fluid to it before installing it. When I worked in the dealerships, the transmissions we replaced with the converter installed were not filled. It isn't going to hurt anything. Just like an oil filter. I always fill the oil filter before I install it.