Plastiguage is the ONLY way to do it as far as main and rod bearing clearances. My concern for you is the severely worn lifter (s) and were'd all that metal go? Or through! (That would be a concern). Gonna require a hot tank and thorough block/head cleaning to be sure, IMHO. The cam is wiped, at least on one lobe, probably.
New cam/lifters, obviously in order, and proper break in on that. I would replace the valve springs anyway while at it, as Marc said.
Personally, I would ensure the seat pressure on the springs meets spec for the cam you're gonna use .Those are all available as a kit, usually. Marcsrollin can hook you up on that! I would put in new main and rod bearings anyway and a crank polish while its down. Cheap insurance. Always polish the crank on new mains and rods.
As far at what clearances to look for on the short block? Dave at A&D, Ralph, or Barry (Obnoxious1) would be the pros, but I beleive if you go .002-.005 over spec you should be fine on a boat engine. I'd lean towards the .002 side, but just me.
Topm posted something recently about ring gap too, but doesn't sound like you need to mess with new rings/pistons.
Ray