Had planned on joining once the boat was up an running but need a little advice in order to get that happening

I purchased a Lewis Tornado as a project, it is a 350 chev with a dog clutch. The engine was too far gone to rebuild (had already been rebuilt once before). Anyhow I ended up buying and rebuilding a Vortec 350 Chev. I have lowered the engine in the boat tonight and have 2 issues thus far.
1) The sump is different to the last and older 350 chev and it is touching the bottom of the boat. It is sitting on the engine mounts but still touching the bottom. How much clearance is reasonable and what are my options here? From what I can see there is no ability to slightly lift the engine mounts given the shaft doesn't have the ability to move up?
2) On the shaft again, does it have any movement at all? Whilst the engine is on the mounts it still needs to go back about 10-15mm to line up with the holes in the engine mounts for bolts to go through. The issue I have is that the dog clutch is hard up against the coupling. Didn't want to get too persuasive with it until I had some advice.
Thanks in advance,
Chris