I have a fresh transmission ready to install so really have no experience with a pristine condition transmission operation. The transmission that was in the truck before I tore it down for restoration acted similar to what you described in 1-2. It would all but drag the engine down. I did have a transmission shop (with the owner being of the age that he was well versed in the H-M transmission) check it over and adjust it before it was installed. I also let him drive it for it's maiden flight. I was led to accept that 1-2 was for tromping it trying to get out of a mud bog or some similar scenario. The throttle pressure adjustment as mentioned is critical. a quarter turn seems like it can be the difference between running all gears within 15 feet and not downshifting when slowing down for a corner. Had to "sneak up on it".

Vibration? that is tough. What U-joint did you use. I know the front half is H-M only. The back half is common with manual transmission u-joint. Did you put a manual transmission u-joint in it by chance? The rear mount is just a rubber isolator in a plate that is sandwiched in a bracket that bolts to trans tailhousing. Maybe take it loose and see if it helps take driveline out of a bind? Have to assume that alignment to engine is still the same as you would be using same adapter plate and dowel pin alignment. Are you sure front mounts are correct and that it has not somehow turned into a more "solid" motor mount? Loosen each bolt a quarter turn to see if improves?

My advice may be crap. But I am sure it will draw better troubleshooting technique suggestions if it is.