As we often say, slowdowns can be a sign of other troubles. As in, viruses, malware, etc. Plus scanning for a virus, etc. won't hurt. One question: do you have off-computer storage, such as CDs or DVDs? If not, that might be a place to start, too. Something is taking up space, particularly random access memory but it also sounds as if there are a lot of directories so there's a lot of searching going on. Offloading some of your stuff may help plus, if there are problems, you'll have things saved off the computer.
.mpg files, .mdb files and others can be large.
Another question is: what's open when you're trying to d/l files? Excel is a particular memory hog, for example