allignment question

Yes.

Just make sure to remove your clamps and jacks before the final alignment check to make sure you weren't moving the rubber mount instead of the motor.

Test

Put the nut back on the rear pinch bolt as you have the front one in your pictures. Tap them down on the back ones, forward or backwards on the front ones depending which way they are oriented.
You wont be able to move the motor until the pinch bolts are loose.
Spray some type of lubricant (WD-40 PB Blaster) on the mounts and work the motor back and fourth(from side to side)till it moves freely.
On the front mount loosen the top nut (top nut is the lock nut) almost all the way up there is a nut the same size under the mount that is the up and down adjustment for the front mounts.
on the rear mounts loosen the large nut (lock nut) several turns. The up/down adjustment is made by turning the square top part to raise and lower the mount. Again here some spray om the rubber parts helps.

I will add to Chris's scissor jack comment, if you have one of the Ford jacks that you put the rod in and turn that works and you can turn it by hand. Forgot that I tried that but ended up not needing to use it.

Just a thought.... Looking at the engine and tranny...I would think it very unlikely that the engine moved when I hit something. I say this because when I try to move it , it doesn't want to go. Could it be that my strut is off or bent? I only ask because it ran pretty smooth before I hit something and now with a new shaft it's off. I think when I move the engine and tranny over it will be fine but am I compensating for a bent strut? I'd rather straighten the strut right? Thanks, Tony.

Nope, I was fortunate enough not to need to use them. I was able to cheat a bit putting the motor I and slid them roughly into place before I put the weigh on them. The couplings were lined up at that point so all that was left was adjusting the distance inbetween them.   The Vdrive was different because you're moving coupling that's on the shaft for a DD. Took me a little while to remember that when I was deciding what to move. First time is a PITA, but next time goes much smoother. I had a helper the first time who did the moving while I checks the results, after that I could check and figure out what to move and it was only about a 20 min process

On the front mounts you can use an 8in C clamp to pull it to the side you need. I'll get a pic up in my thread later tonight or PM me a mobile number and I can send it from the phone.

Tony,
You are very welcome!

Ok so I want to " bump" the motor and trans a little to port but can't understand the adjustment on the motor mounts. Sorry but I can understand up and down, but port to starboard kind of confuses me. All I see is the up and down. Can someone explain. I watched Pete's video and it all makes sense but you cant actually see what he is explaining in the video. He says its a "split" piece that will move port to starboard in the rear but I cant see that. Sorry i'm still a noob. 89 Ski Nautique. Thanks, Tony.

In case youre missing it in the above posts, the first step in aligning the powertrain is determining where the shaft spins freely in the strut. Letting it settle under its own weight and forcing it any direction (trying to mate the transmission coupler, etc) are no-no's. It will not find its happy spot "on its own".

Once you find where it spins freely, support it in that location and move the powertrain to match it. If you miss that first, critical step, then whatever you do afterwards doesnt matter and you'll end up with a misaligned shaft.

I would probably start out kicking the front of the engine to the port a touch, 9 out of 10 times this will cure it, I try not to break the complete engine loose until I attempt kicking the front over. then proceed if that doesn't cure the alignment

It really depends on where you need the engine to go, it take a little playing around with and measuring to figure out the way it moves. Once you get that it's not hard to guide it where you want. I don't care for the rear PCM mounts, with my Crusader I could put a C clamp on each mount and move it easily. Can't do that with the rear PCM mounts. I also noticed that it was easy to move the studs in the bushings instead of the motor. Keep an eye out for that, though I had it a couple of time only to have the bushing move it back to where it was when I released the clamp.

Watch Pete's video, it may or may not sit in the sweet spot in the log. Push it back so the couplings don't touch and see if it spins best there or some where else. Once you figure out where that spot is you migh have to use something to hold it there while you move the engine to that spot. A ratchet strap worked for me. Once the engine is close there was a lip inside my coupling that would keep them close enough without having the strap on while I finished adjusting for the last few .000ths.   If I took the coupling further apart the shaft would drop and hit the sides of the log.

Ok two pics here of new shaft. I thought I would slide it in and see how well it lined up. It looks like I need to slide my transmission to port a little. I can move the shaft over by hand and line it up fine but I thought it should line up on its own if the alignment is right. Right?? What do you guys see? It spins freely when connected but I think it should line up without me pushing it over at all right? Thanks. Bones.