Mike.......in real life there is a sequence of prop shaft alignment procedures that we can consider & use in model work
...may sound a little long winded but it will work
1. You appear to have adequate alignment clearances where the prop tubes intersect with the hull base plate
2. There does not appear to be adequate clearance where the prop shaft intersects the bulkhead aft of the motor........this clearance should be increased
3. After the motor is fixed, the next is the P bracket.....lock this in place, perform the next step 4. & if OK, bond the P bracket mountings with your chosen epoxy
4. Turn the motor over by hand.....it should be free to rotate....if these new style motors exhibit too much magnetic gauss/resistance ...run the motor or minimum voltage & check the current draw
5. Next is the bonding of the prop tubes where they intersect with the hull base plate
6. You could consider some resilient tube washers where the prop tubes intersects the bulkhead aft of the motor
7. With any epoxy mounting, thermal stresses can occur between components & minute distortions occur
8. Turn the motor over again as @ point 4. ... you may meed to release the motor mounting & turn the prop shafts by hand without the motor to confirm the shaft freeness
In real life these days, many large diesel engines are then shimmed & epoxy grouted to attain optimal shaft alignment
...................good luck.......Derek