I'm trying to install a engine in my 2001 explorer, the converter seems to be seated properly in the transmission, however I cannot seem to get the engine to seat all the way to the transmission housing. The flywheel bolts are aligned and go through the flywheel, but that's as far as I can get it.

 

If you are trying to install an engine that is not an exact replacement, same year same model etc., the hole in the flywheel could be a different size , the converter tangs might be different if you are not using the original converter with the original trans and on & on. Ford is known for making production changes mid year and one little item could be different. I would make sure the converter is all the way in to engage the pump gear fully.