Just saying that while a logic board COULD cause these problems, it's pretty unlikely. In the two instances where I've seen a performance issue tied to the logic board, usually the system is VERY slow to boot, often times won't boot consistently, but once it does finally boot, for whatever reason, it runs fine.
And the number of viruses (and worms, trojans, malware, etc that people often lump under the general term "virus") that can actually attack OS X can be counted on one hand pretty much. All but maybe one or two are proof of concept, and the one or two that aren't, require considerable amounts of user interaction to install. Granted at least a few people have been fooled by the Mac Protector thing, but I would put that possibility of a virus at just this side of impossible.
The permissions thing is also unlikely to resolve anything, but it takes maybe 5 minutes to try, and there's virtually zero down side, so why not.