Software Issue After update (Aero, Safe mode boot, Software currupt)

So First off, I am sure most of you who are looking at this will think it is an easy fix, and trust me I wish it was. I have spent the entire day before this post searching for common fixes to issues, with no luck.

First off, here is the scenario:

I went go get on my PC that has been running flawless since December 2010, and the first thing I notice is it came back from sleep or idle, whatever you want to call it. This seems to happen now and then and I believe it happens because windows installed an update over the night (Wednesday 2/27/13). Normally this is no big deal, I go about my way and all is fine.

So I noticed that some open files I was working on in excel have duplicates, one set is read only, one is not. I closed all that down and we were all set. The other big thing is the Aero feature was dead. So I went online and hit ALL the usual fixes, running the diagnostic, downloading the specific MS diagnostic tool, resetting the service multiple times, restarts, even some registry updates I found. NOTHING worked. The interesting thing is the only part of aero that is not working, is the glass feature, and the peek feature. All the mouse icons and other attributes seem to be working.

I have an Nvidia GTX 460 card, so I updated to the most current form of the drivers, nothing. I delete the drivers and install the original CD drivers, nothing. I then delete the driver and try to use driver sweep to remove them. This is when I notice that I can not boot into safe mode. It just restarts when it gets to a login screen.

The other thing I noticed is my two installations of Autocad 2011 and Inventor 2012 are DOA, they fail to launch and brings up the error report window. So begrudgingly I reinstall and get the same error. All other software works flawlessly.

So I am at my wits end, I wanted to try a system restore to before the changes but the default system restore size only allowed 1, and that was the original update at night. I made a change and that one was gone. I only have an OEM win 7 disk, so it appears I can not do a repair, and all I can do is do a full reformat. I am trying to avoid this route if at all possible, so this is my last ditch effort to find an answer. I have searched these forums and nothing works as of yet.

Thanks for any help.

P.S.
I have also been getting an 1910 error when uninstalling software
I have run a memory test
I have scanned with AVG free & Malwarebytes

Custom Built PC
Win 7 pro ver 6.1 (build 7601: Service pack 1)
GIGABYTE GA-X58-USB3 LGA 1366 Intel X58 USB 3.0 ATX Intel Motherboard
Intel Core i7-950 Bloomfield 3.06GHz LGA 1366 130W Quad-Core
G.SKILL Ripjaws Series 12GB (3 x 4GB) 240-Pin DDR3 SDRAM DDR3 1333 (PC3 10666)
EVGA 768-P3-1362-TR GeForce GTX 460 (Fermi) Superclocked 768MB 192-bit GDDR5 PCI Express 2.0 x16 HDCP Ready
PC Power and Cooling Silencer Mk II 750W High Performance 80PLUS

Mushkin Enhanced Callisto Deluxe MKNSSDCL120GB-DX 2.5" 120GB SATA II SSD
1x Seagate Barracuda 7200.12 ST31000528AS 1TB 7200 RPM 32MB Cache SATA 3.0Gb/s
x2 Seagate Barracuda XT ST32000641AS 2TB 7200 RPM 64MB Cache SATA 6.0Gb/s

Essentially this, except mine is pre-service pack 1 and I updated through windows updater. It is a system builders version.

Microsoft Windows 7 Professional SP1 64-bit - Newegg.com

Here is the output file, I got some dupes, so I kept them both.

I did get some errors about files in use, and one that would close the program.

I re-ran the tool with everything closed after a restart and it all went smoother. Here is the newest zip.

I am running:
Photoshop CS4
Illustrator CS4
Premier CS4
Lightroom 3
Adobe acrobat 9
The latest acrobat reader

Any ideas?

I do not mean to be pushy, but I need to get this fixed. I am open to ideas, otherwise I am going to have to reformat my OS drive.