904 Pump Housing Leaking Between Ports

It is normal for some bleedover in automatics, but how much is the question.
Have you tried putting bolts and nuts in those two bolt holes and checking it?
It might make you feel better about it if you can see it clamped.

Since there is no gasket between the pump halves I would expect bleedover in those places especially without all the bolts in it.

Just snug them a little, and not as tight as you would put the actual bolts in.

If the front drum fits the stator and rings well, and the direct drum input shaft rings and bushing fits good I'd be ok with putting it together.

One thing you might try is to put it in and when you air chk the direct drum see if you can turn the forward drum while the direct is engaged.
If you can turn it, I would feel fine about it.