How to make sure my system is clean?

I am not seeing any malware, however:

I strongly advise you to cleanup your Desktop. Remove eveything but links to run programs. Do not download and save programs here and defintely do not use it for long term storage. You need to keep ComboFix.exe here for now as we need it, but we will be removing it when we are finished with your cleanup. A cluttered Desktop is malware's playground and it can also cause performance degradation especially when you start saving large files here like you are doing.

You should also have uninstalled:
Viewpoint Media Player

Please tell me what issues you are currently having.

If you are not having any other malware problems, it is time to do our final steps:

1. We recommed you keep SUPERAntiSpyware and Malwarebytes Anti-Malware for scanning/removal of malware. Unless you purchase them, they provide no real time protection. They are useful as backup scanners. They do not use any significant amount of resources ( except a little disk space ) until you run a scan.
2. If we had you use ComboFix, uninstall ComboFix (This uninstall will only work as written if you installed ComboFix on your Desktop like we requested.)
   
   • Click START then RUN and enter the below into the run box and then click OK. Note the quotes are required
   • "%userprofile%\Desktop\combofix" /u
     
     • Notes: The space between the combofix" and the /u, it must be there.
     • This will uninstall ComboFix and also reset hidden files and folders settings back to Windows defaults.
     
     
   • Delete the C:\combofix folder from combofix (if it exists)
   
   
3. Any other miscellaneous tools we may have had you install or download can be uninstalled and deleted.
4. If running Vista, it is time to make sure you have reenabled UAC by double clicking on the C:\MGtools\enableUAC.reg file and allowing it to be added to the registry.
5. Go to add/remove programs and uninstall HijackThis.
6. You can delete the C:\MGtools folder and the C:\MGtools.exe file. You can also delete the C:\MGlogs.zip
7. If you are running Vista, Windows XP or Windows ME, do the below:
   
   • Refer to the cleaning steps in the READ ME for your Window version and see the steps to Disable System Restore which will flush your Restore Points.
   • Then reboot and Enable System Restore to create a new clean Restore Point.
   
   
8. After doing the above, you should work thru the below link:
   
   • How to Protect yourself from malware!