I've got a bunch of mods and have figured out how to use BOSS well enough to ensure there are no fatal errors or anything, but am at something of a loss with the dirty edits and minor recommendation tags and such. I have my setup at the point where Boss is all green (excepting a couple unrecognized) and TESEdit makes it all the way through its check without failing (but, again, no idea what to do with the minor problems/recommendations and stuff) and I use a bash patch though I don't really know what it does.

Up until now, I've pretty much just ensured there are no major errors and gone ahead and played ignoring the other stuff because the game was working fine. Now, however, it has lately started freezing for a few seconds pretty commonly. I've tried uninstalling the recent mods, but it seems to be related to save bloat as a real old save doesn't do it.

Does anyone know if this is likely because of the unnecessary files and hangups that I haven't done anything about/have a recommendation on how to fix it?

If it would help (and you let me know how) I can post a copy of my BOSS log or whatever else.
Thanks.

First of all, uninstalling mods can cause save game bloat, among other damages if the mod edited any vanilla scripts and such.

As far as mods with dirty edits, you'll probably want to notify the original mod author first before cleaning, and if you can't notify the original author for whatever reason, then I suppose you could clean it some, but ONLY if you know the mod inside and out for the most part (uninstalling and reverting to a save from before the mod was used is usually better and recommended). I generally wouldn't recommend cleaning mods not developed by you unless you know what you're doing. You definitely do not want to clean mods that the mod authors say are already cleaned, as they can contain dirty edits that are intentional and will break the mod if cleaned. The Unofficial Patches are prime examples of mods you NEVER clean.

I believe it is recommended that you clean Update.esm and the DLC esm files, but they must be done in a very specific order, as shown http://www.creationkit.com/TES5Edit_Cleaning_Guide_-_TES5Edit#Order_For_Cleaning_Bethesda.27s_Master_Files. This link also can get you started towards gaining any knowledge of TES5Edit you didn't know before, and I suggest doing some research on how BOSS works ASAP since you stated that you don't know what it does, which doesn't sound good.

For the most part, dirty edits are usually just minor edits to vanilla cells like interiors because a lot of people out there don't realize how easy it is to "modify" these cells when they look at them. They are very annoying to look at and really should be cleaned out with TES5Edit (or better yet, they shouldn't be made in the first place), but are usually relatively harmless and probably won't break your saves. I still hate those kinds of edits, though. Certain kinds of dirty edits, such as navmesh deletions for instance, can be far more serious due to the nature of their size and how many mods may be reliant on them. Deleted containers, doors, markers and other possibly important objects and references can be very bad as well. Deleting vanilla objects is actually frowned on in the modding community.

One last thing. Poorly implemented scripts can cause save game bloat.