I'm about to put my boat back together after a 2 year layup. The engines are 540's, 700hp@. It was winterized properly and oils changed before layup. I am guessing that I will have to drain the fuel tanks, change filters and pull carb bowls before attempting to start. My bigger issue is I need to re-install the extension boxes and drives and I have never done that before so I don't know how to properly seal them, any torque specs for the transom bolts etc.. I have new foam seals but should I also use any type of sealant on them? Any more advice would be appreciated, THANKS!

I would torque the extension box in the same pattern, number of passes and torque the transom assembly calls for.
what box and drive do you have?
what engine mounts?
i would also look real hard at alignment.

I have Stellings boxes and Imco SC drives. Transom assemblies are Merc HP's. Alignment isn't an issue since I am running drive line with driveshafts. Engines on rail mounts. Do you happen to knoe the torque spec for the transom assys?

25 ft lbs for ext boxes and pretty much anything that is bolted through the transom