Shoulda been investigated the first time a coupler went bad. Misalignment is usually why they fail.

Did you find out if the angle changes by rotating the crank 90* ?

I didn't unfortunately, but good to have ruled it out.

Theres a special alignment disc you can purchase (i'll try to scare up a part number). It fits into the transom assembly and then the alignment tool goes thru that. The bell housing has to be straight left and right and 90 to the crank or the shaft wont go thru the bearing and then into the coupler.

Kinda proves the gimbal bearing isnt all wacked out either since the engine looks low in front and to the right.
guess it also shows if your rear mounts have sagged.

post up the engine drive and transom serial numbers so these guys can help you figure out if you have the correct stack on the rear mounts or not as well.

also if that's pvc you'd be the first guy in the world to have a straight piece, use the alignment tool ?

No worries, I have the tool. This pipe was just to give it a rough alignment when its way off. The tool goes in and out now after some adjustment, but its still off to port side and that's not good. Up and down is good.
I've got the old motor mounts with new double wound spring washers and fibre washers. That doesn't fix the side alignment unfortunately.

If your chewin up couplers and having a problem aligning I would take a hard look at your transoms condition.

are the nuts that secure the transom torqued the same amount,sounds like 1 side of the transom is squeezing in more than the other.remember,1/8" at the transom,turns into an an 1" farther out.

Yes it's torqued to spec. From what I could see by just measuring to two top bolts, the port side protruded 1 mm shorter from the nut. That adds up to the misalignment. Also turned the engine as far as I could in the front to the port and it got a little better.
The alignment tool now went in absolutely perfectly, so decided to bolt everything down, put the drive on and going to sea trial it to see what happens.

An update, it still vibrates on sea trial. Lighter but faster vibrations going forward, slower and more prominent going backwards and turning. The harder the turn going backwards, the more prominent the vibrations gets.
The only thing I haven't replaced is the outdrive so that's probably next on the list. I'd prefer to be able to try with another outdrive but I just presume no one is going to lend it to me with the risk of it taking some damage if it's an alignment issue.

I've had the same problem on an older MCM Alpha 1, could never get it to aligned laterally. I finally gave up after fighting it for a few seasons, pulled the engine, the inner transom plate and it became immediately evident that I had a soft (yes water) transom on one side and not the other. I rebuilt the transom and it was amazing how nice the shaft engages the coupler!
That may explain your variation in exposed threads on your fastener set. Good luck, hope I helped a little!