Clean boot disabled aero theme & Internet connection, help?!

I run a windows 7 64 bit home premium machine with a Nvidia Quadro 440 graphics card as well as a Nvidia inboard GeForce 7025 card I installed windows myself and its been working great for the last two years until a few days ago. First it wouldn't shut down properly and got stuck on the logging off screen for about two hours. Then I noticed it needed some 10 updates, which after some effort I managed to install, all apart from one non essential Nvidia update that wouldn't for the life of me update, so I just left it. Then I noticed iTunes not being responsive, it took several attempts for it to recognise my iPod and after various attempts taking some six hours I finally got my iPod updated, i have the latest version of iTunes. I decided to have a go at fixing this. Long story short, I performed a clean boot and now, after I enabled normal start up again;
1) My aero theme has been disabled and is un available for selection,
2) I have lost my Internet connection and the set up wizard isn't working,
3) I can't perform a restore,
4) The windows update service isn't running,
5) And my audio driver seem to have gone too.
6) And when I try to restart the computer, it switches from logging off to shut down no problem, but then gets stuck on shut down.

I need help please, any will be appreciated

Hello thys and Welcome to Seven Forums.
You have some kind of corruption in the system files. This could be signs of a failing hard drive. Here are a couple of things to try
SFC /SCANNOW Command - System File Checker
Press the start button, navigate to the Command Prompt or type cmd in the search box. Right click on the Command prompt in the Start Menu and select Run as Administrator. Type :sfc/scannow and press Enter. Let in run and fix errors if any. Also download Download Hard Disk Sentinel and use the free trial to check out the hard drive.
Report back and post screenshots of the hard drive health.
Geeks are like London Busses there will be another one along shortly with further advice. :)

Thanks, I'll give that a go, but I can't download anything, because even though the Internet cable is physically plugged in to the comper, the wizard doesn't seem to recognise it?

Try the scan and file recovery and see if anything is corrupted first.

You couldn't have turned off Aero or affected any system functions turning off 3rd party Startups in msconfig>Startup. Did you turn off anything in msconfig>Services without first hiding all MS Services?

Rightclick on the internet connection icon in bottom right System Tray to run the Troubleshooter, check Device Manager if the ethernet driver is installed.

Your sound would not stop working by turning off sound software at Startup. Check the driver in Device Manager to see if it needs updating.

In addition to working through Indiana's suggestions given before, here are other Troubleshooting Steps for Windows 7

Thanks for the advice Greg but I don't even have Internet running in the tray. I've tried system file checker, but when I hit enter it just gives me another prompt and nothing happens. I've tried hiding and un hiding MS services and nothing again. I've also noticed, and it never done this before, every time I go to use either cmd or msconfig the user account control prompt pops up asking if I want them to make changes to my computer? As I've said, it never asked me for that before. Still in the dark here, any other suggestions??

The UAC setting has apparently increased. I would leave it there.

You will have a connection icon in the bottom right System Tray, rightclick it to run Troubleshooter.

Type Aero in Start Search box, run the Aero troubleshooter from results.

Run a full scan with Malwarebytes

Replace your AV with Microsoft Security Essentials and run a full scan. If you have a bloatware AV then google for its removal tool to get the whole mess out.

Report back on your progress on these and other Troubleshooting steps you should also be working through to go over it thoroughly.

Thanks for all the advice, I gave up eventually and just took it to a shop