Have never seen this with an outdrive setup. Boat is a Formula 292 and has twin 5.7's and Bravo drives. There is no adjustment to align the drive, its either dead on or its off. What's missing?

All off shore mounts are like that, mark the holes before removing and it goes back in the same spot

Solid motor mounts, considered very strong, Dont really need them with those small motors. ...but how to align??

Swap for standrad Bravo setup

Pedestal mounts are adjustable, the rubber can sag and need to be realigned. If those move you have serious rot issues.

The guy said before motors were removed the alignment was perfect, couldn't ask for any smoother. Motors were rebuilt and bolts went back in same holes, and alignment bar does go in but just not as smooth and requires more effort to remove bar

Is there rubber pad between mount and motor that can be replaced?

loosen the bellhousing bolts and tap your alignment bar with a rubber hammer side to side and up and down to align the rear of the engine to the bearing

Edit: no rubber on an offshore mount that Ive ever seen

ok no rubber on front, only on rear mounts. Never would have thought this setup with a Bravo drive, transmission or jack shaft sure. I'll pass info along Tx

The alignment is set. If it’s off there are other issues.

depending on what rear mount you have that might be causing an alignment issue .mercury has two different rear mounts and I have seen the new style mount with the grooves on the bottom out of spec right out of the factory and typically will need to shim that area
that mount requires no spring only the washer
also my recommendation to you before you install the drive would be to disconnect an ignition wire to get rid of spark ,seat the alignment bar all the way into the gimbal bearing and have someone turn over the engine
watch the end of the bar while the engine is rolling over
if the alignment bar moves you have an out of round coupler and eventually it will fail
an out of round coupler can also cause an alignment issue