Hey girl - yep, you should be vacuuming a tank like that like nobody's business.
I would do a massive vacuum, taking out along the lines of a 40-50% of the water. Someone may disagree w/this just because of the cyclage mess up, but this is what I'd do and just monitor levels after you do the massive cleaning)...
Someone else could suggest a regular vacuuming schedule - cuz I don't have any tanks that I need to vacuum, but I used to so I know you should be vacuuming.
If I were you, I'd treat the whole works with Maracyn and Maracyn Two at the same time. They're perfectly safe to use together, and with those 2 you pretty much cover most illnesses that they could be battling.
It sounds like it could be columnaris creeping around in your tank.
My most recent rescue, Jack, had oodles of cottony patches all over him - some of them were even growing out from under his scales, causing 2 of his scales to stick straight out. He also had severely shredded fins and pinholes. After just one round of M and M2, the cottony junk is gone and by all appearances it looks like he's on the road to recovery.