Some drops are common, although they may suggest keeping an eye on the hard disk. They can be related to OS or other software activity during the scan, although one drop occurs always in the same place in all three scans, so there may be some kind of trouble there; unfortunately doing a certain diagnosis in this case is really difficult, especially if SMART parameters are okay. I had only a case where the hard disk was deemed perfect by diagnostics and benchmarks but it was, in reality, faulty, just because of a performance drop like that, more severe perhaps (I can't exactly remember) and plenty of hard disks that showed the same drops that had no problems at all. Only a direct comparison with another HD with the same exact content would help making a decision. This isn't hard to do, you only need some imaging software (like, for instance, Acronis Migrate Easy, but there are others) and a new HD, but I realise you need to have some stuff available, and this may not be the case.
I'm afraid I've run out of suggestions. Since I do tech support/administration for business pcs and networks I'm afraid I've run out of suggestions, but hardware buffs may help more.
I'd personally try to strip down the system to a minimum shutting down unneeded software and services, even uninstalling some stuff, especially programs that may interfere with input/output activities (such as indexing software, firewalls and antiviruses), but this doesn't sound like the culprit in this case.
Anyway I'm impressed with the job you did.