Alex, I know I saw it the other day, but I've slept since then . . . it does have the deck lid with 4 sets of slots doesn't it? And I think it had the flaps in the shroud, didn't it?
I'm pretty sure Kyle and I check all the normal easy to spot stuff like that and missing tin, bad engine compartment seals, trash in the fan, a loose belt, etc.
If all that stuff is good, normally it's an ignition timing problem or it's running too lean. Didn't you say you had just put that carb on it? I didn't realize it was oversized jugs . . . maybe the carb is just too small for a 1641 . . . or maybe it needs a bigger main jet. At any rate if you did in fact just install the carb and the overheating started right after that, I'll bet it's got something to do with the carb.
Again, I've slept since then and can't remember exactly what we did and didn't check. Maybe I missed something obvious . . . but at any rate, we do need to figure it out and get it fixed or you'll be needing a set of pistons and cylinders soon . . . 87mm jugs can't take a lot of heat (neither can dual port heads)!