I blame GFWL

So what happens exactly when you try and update the game?
Try downloading the latest version of GFWL.

Well, the problem is that all of the games menu's are black, and none of the game's Text appears.  As if I'm missing visual layers, or something..  they're just.. not there.  The only way I know I'm at the character select, is because I see the portraits..  over a black screen.  And, everything is completely mute.

Other than updating graphics and sound drivers I don't really know of any fixes, not without sitting down and looking at the problem myself anyway. I assume you are using a laptop so you could try checking you power managemnent settings as they might be limiting the GPU or something. 

Edit: try posting in the CAPCOM forum they have a massive thread for issues in he PC version http://www.capcom-unity.com/street_fighter/go/thread/view/7411/27973929/SSFIV:AE_PC_Issues_-_One_thread_to_rule_them_all?pg=1

Also try looking at this thread

http://shoryuken.com/forum/index.php?threads/super-street-fighter-iv-ae-pc-big-bug-thread-post-your-ae-pc-issues-here.140594/#post-5538346

Seems like the PC version is just a buggy mess all round, I mean a 103 page thread for a game that probably sold less than 100k copies on PC? that is insane...

I'm on a desktop, and this computer's not letting me update my drivers, my anti virus software, or perform a windows update... It's not letting me update a damn thing.  I give up.

It is... but steam actually has quite a nice collection of Mac games.

You can get pretty much all of em on a PC... but still.

I just don't like Mac/PC gaming so I doubt it would've mattered even if they did.

Sounds like your problem has less to do with PC gaming and more to do with having a brokendown PC.

Which is what I was going to suggest might be the case.

It's not broken down. It's fairly new. Doesn't make weird noises, and is actually pretty fast... Except when it comes to running games. The guy at the store asked, and I told him I wouldn't be playing games on it anyway... Or, so I thought.

Anyway, I think I may have somehow locked myself out of permissions, and, maybe there could be a virus, or something... So, I'm just going to wipe my computer clean after backing up the stuff I want/need to keep. Then, from there, I'll update everything, then, put all my files back.

Any warnings would be appreciated, before I screw something up.

Okay, after wiping the HDD to factory, and installing the game after updating the driver... it works... No clue if the game is running at 60FPS, but it feels like it.

But, now... there's still one last problem.... my PS2 controllers don't read... Sure, playing on the keyboard could be nice, and all, but, I can't stock more than one fuhajin, and I can't pull off ultras and supers reliably. What do I need to do to get my PS2 controller working?

Are you positive your adapter is working?  And if you have a 360 might as well use the 360 controller.  Trying to get a PS3 controller working is a bit of advance work I doubt you'd wanna put up with.  If not this controller is decent enough if you see it in stores on sale: http://www.logitech.com/en-ca/gaming/controllers/7360