Vintage BMW Motorcycle Owners

I first made sure that all clutch parts, plates etc. are centered.
Then I attached the tranny like this: I put it on the tips of the studs, then with long nose pliers I pulled the push rod inwards into place, to sit inside the square hole that is in the plates center. Then while in gear and playing with the rear drive coupling flange, I pushed it into place making sure the engagement of the toothed shaft towards the engine.
All went well except that there is a gap on the bottom of the tranny. The upper side fits good to the engine, the bottom part won't get any closer. I told my boy who helped me out here, that if this was our BSA (standing patiently beside us) I would use a big hammer, but here at German engineering there is definitely something wrong, so I stopped immediately (and the nuts on these pictures are not tightened down, of course).
I will appreciate your ideas of where to search for the problem.
BTW, it's our 3rd attempt with this result.

Have you tried loosening the bolts and wiggle the trans. vigorously up/down & push in.? Is the trans. cocked on the..... Going that far in to position I would try tightening the lower bolts first....criss cross.

Have you hooked the clutch cable up yet? If you have try cycling the clutch hand lever several times and see if that realignes the clutch pack.

Yes, all of these methods have been tried.

Forgot to mention that:
Years back I took the tranny out and had no problems getting it back again.
A new clutch and push rod are now installed, bought from Mark Huggett.
Also there's a new pressure plate.
I thought to myself that the bottom may not be clinging properly because it is pressed against something springy in the clutch system? And closing the nuts by force is necessary here? I could not feel any thing spongy.

Have not tried with the clutch hooked on yet.