Seems likely that there is something in the OS that has become bent out of shape.
Archive and Install doesn't exist anymore with 10.6. At least not as an explicit option. I believe with 10.6 it can basically do an in-place reinstall. Just wiping out key bits like the System folder and laying down fresh versions without having to mess with your installed apps. In any case, people can search all day long and be unlikely to find the archive and install option in 10.6.
That all being said, the OP's problem sounds like a failing HDD to me. Early stages, which is good. They also appear to have backups which is also good. I'd be willing to bet there's been a slow degradation of performance, but probably gradual enough the OP isn't even aware of it. I'd recommend taking it somewhere to be looked at, because odds are pretty soon it's just going to crap out completely. Hopefully it's under an Applecare agreement, because otherwise if you don't source the drive from Apple, it won't have the right thermal pin configuration, and your HDD fan will default to running at full speed the whole time. It won't hurt anything, besides wearing the fan out faster (and being under the logic board, it's a PITA to replace) and being obnoxiously loud. But it is ultimately just a 3.5" SATA HDD, so if you don't mind the fan noise, it can be replaced with pretty much any drive you buy at a store.