Yes, you need to remove the drive again. This time I would make a cart for the drive. Set up the height so you can trim the drive horizontal and you can raise/lower the front of the trailer so the drive sits on the cart. Then you'll find it's very easy to remove and re-install. On the engine mounts I would try to get both sides at equal height, then adjust both up or down until the alignment tool slides right in. With grease on the end of the alignment tool, if you see deeper spline marks on top of the tool, raise the front mounts. You don't need to mess with the rear mounts.
The nuts on top of the motor mounts are meant to be lock nuts to prevent the lower nut from moving.
Thanks. I'll try to get around to removing the drive again over the next few days. The main reason I'm concerned about the rear mounts is because I removed and refitted this engine a couple of years ago, I remember having some confusion about how the rear mounts fit together.
When I've removed the drive will it be OK to leave it on it's side without dropping the gear oil? I'm thinking too much gear oil might move up to the upper end of the drive but it'll be months before I use the boat again so even if that happens the oil will drop back to where it's supposed to be when I reinstall the drive.
The top nuts on the front mounts are locking nuts, the nut(s) below don't seem to be locking nuts... But there are 2 nuts below on the port side and only 1 nut below on the starboard side - maybe the starboard side dropped if the 2 nuts below are supposed to be torqued together to lock each other?