For lift set up -
When you have a V-Drive boat you need to make sure you don't let the boat hang too far back on the lift - lots of weight in the engine. DD's you can let the boat be further back with fewer issues.
Bunks, You want to make sure that the bunks are high enough that tracking fins/underwater gear won't foul up.
Otherwise lower is better. You also want to transfer the measurements of the trailer bunks to your lift. MC has those bunks measured out to support the boat under the stringers in the hull - which is very nice. Cheat and set hose up.
Also you want to make sure the boat is centered on the frame so do all measurements based off a center measurement.
Finally - some lift companies piss me off. Shore station being one of them. They provide those carpeted "side" bunks to center the boat on the trailer. While they seem nice - they are below the rub rail and mess up your graphics on the boat, particularly the vinyl Mastercraft logo, and raised logos.
You want to replicate what your trailer guides are like. Get U bolts and some 1.5" galvanized pipe, set it up with PVC plastic tubing slipped over so that when your boat is coming on/off the lift the PVC will "roll" along the rub rail instead of those bunks messing up the hull.
You also need something to keep you from coming onto the lift too far, this will make sure that you are on the lift all the way, and that no one will get the prop into the lift.
Easiest I've found is to place a PVC pipe crosswise so it contacts the front tracking fin. It will bend out of the way if you bump it.
Neighbor has a 4X4 treated board screwed to the lift frame to do the same, but I've seen his mother run the front tracking fin into that hard.