1) While it's always been quite laggy, I'd say it's gotten worse since I installed qBitTorrent and used it to try to get some programs via torrent. I assumed it might have been infected with some malware or virus, but as I said MalwareBytes supposedly removed everything and nothing's changed. I have also tried several other things suggested online, like deleting programs I don't use or files I don't need, but it doesn't seem like memory space is the problem. Regarding IE in particular, I never use it, so I have no idea why it isn't allowing me to download anything.
2) In safe mode it was much faster, opening programs almost immediately. Only Spotify crashed for some reason, but Spotify has always been slow for me. Even Firefox, which previously I couldn't open at all, worked fine.
If there's any more info needed just let me know, and thanks!