Thanks @Luke, I'll double check but I think they are all up to date. I had also tried pulling a bunch but after I would log into a session, I would just get a spinning wheel. Also, I noticed that at the top of my screen were only "Home" and "Favourites". Everything server side works fine though.
One other odd thing I noticed. When I went back to 3.5.3, the only plugin showing as installed was Slack. Could that have anything to do with the database upgrade that was run when I went to 4.0.1? When I flip back to 4.0.1, all my plugins show up again as expected.