After lots of trial and shaving bits off, I got the back end of the new engine bearer down to the same level as the other side.
At least the front end was fixed at the correct height easily as a datum point.
I then glued it down and dropped the metal engine cradle in to make sure it was in the correct place while curing.
Yesterday I made plywood shelf for the battery box to sit on. The rest of the under berth space provides great storage too.
The blocks locate the battery box, and there is a strap to hold it down.