I moved the engine out of the way to try and figure out what was causing the problem. I determined my transom was not molded out of square to the hull. The next thing I did was to use a length of aluminum angle 1/8" x 1 1/4" x 4'. Without fiber washers I placed it on the mount tabs with the angle down and against the mount ends parallel to the inner transom. On either side of the TP to each end of the angle stock, I got a constant reading of 4 1/8". Now I know the TP is flat and no variations on the inner transom. I was able to determine my stringers to be perfectly perpendicular to the transom. The engine is back in place and only slightly off center to port. I can live with this. Maneuvering the bearing with the engine made a difference. I did realize I had the front mounts adjusted much too low. I'm amazed I ever got the bar to go into the coupler, The tool now slides in easy with no binding. I think it's as close as I can ever get it! I still think something is weird someplace, but how many times can one check and recheck before going insane? Now I'm ready to set up my headers and cut new holes for the tips.Thank's for the interest and all the advice!

Glad it worked out, may never really know..Boats...

If this is a V bottom is the alignment shaft parallel with the bottom of the boat?
If the rear mounts sag the shaft will show proper alignment but the front of the engine needs to be real low to do it.
You can't have anything out of alignment and have the rubber coupling live.
If you are going to run higher than stock HP you will blow the coupling if it is not properly aligned.

Get it on the water and run it. If no vibrations at various rpm's wouldn't worry about a thing. Some boats right from the factory are probably off a tad bit from time to time but who'd ever think to check unless they experienced some type of problem.

I have a V bottom that gets slightly rounded toward the stern. The coupler and flywheel housing is new though it was bought 5 years ago. The bushing are fine. I bit the bullet and ended up shimming the left side of the TP with 1/6" stainless stock. It worked out well and made a difference. The alignment moved right, and it looks much better. Surprisingly, I put back the double spiral washers and raised the front mounts. My friend machined a length of 3/4" pipe for me to use as a guide with a snug fit. It's showing me that my alignment is dead center and the tool seems to agree. The attitude of the engine even looks better now. If I don't have it right, I will find out soon enough. I'm very confident it's as good as it will ever get! ph1971 suggested the engine should be 90 to the transom angle. How can that be possible when the gimbal bearing housing does not follow the angle of the transom?