Driveshaft alignment? Moving strut? Shimming motors?

[thefishingfreak]

I've also asked this on noreast.
The New Cutlass bearings are pressed in and shafts are cleaned up and installed.
One shaft slides perfectly up thru the strut and into the stuffing box as strait as a laser.
The other one is a good 1/8"- 3/16" off from lining up and takes so much force to get it thru the packing box it basicly gets jammed. It was like this all last season.
Should I remove the strut and clean up the 5200? See if there's enough play there to align it with a simple re-positioning of the strut? Re-5200 it down and lock it up?
Second question, how critical is motor to shaft alignment?
I've heard of feeler gaugeing the Shaft coupler to the tranny for precision alignment.
On One motor I will have enough adjustment in the mounts to get it dead on. . The other I will have to shim the motor mounts on the stringers as it's at least 3/16" off from the stuffing box and the shaft center to the tranny. That is also the strut in question.
Third question
Should all these adjustments/ motor mount shimming be made in the water? I know the boat flexes somewhat