Yes,if you did a full OS reinstall,you would have to reinstall all applications.
The tutorial I linked to is not a full reinstall.It is geared more to being a repair install,the way you used to be able to do a repair install of Windows XP,though Microsoft since decided to do things differently.
Some things would be returned to default if you tried the repair(upgrade) install.They're listed in the red/pink box.
It is a bit drastic,though,so you ought to avoid trying it if you feel uncomfortable with it.

Spybot and MalwareBytes are both very good to have,but neither one is an antivirus,and an antivirus is needed.There are some free ones available.
AVG:
http://download.cnet.com/AVG-Anti-Vi...=dl&tag=button
Avast:
http://download.cnet.com/Avast-Free-...=dl&tag=button
Avira:
http://www.avira.com/en/avira-free-antivirus
If you decide to download an antivirus,please only choose one.It's possible more than one antivirus installed at a time can conflict with one another if they both have real-time protection running.

Agnitum and Comodo are both good firewalls.Another good one is Zone Alarm:
http://www.zonealarm.com/security/en...-za-signup.htm
The free one is over to the left.The button appears to be greyed out,but if you click it,it will take you to a download page,with instructions.

No,I don't believe the problem is from any conflict with Malwarebytes and Teatimer.The startup entry in your startup list is Malwarebytes Anti-Malware Reboot,and is listed on this page as being used by Malwarebytes's Anti-malware to perform an action on reboot.
http://www.bleepingcomputer.com/star...exe-22288.html
I believe that startup entry is for some cleanup action it will perform after you reboot.
I don't see any entries in your startup list for MBAM's Real-Time Active Malware Prevention Engine.If you don't have the Pro version of Malwarebytes,then the Real-Time Active Malware Prevention Engine isn't included with the program,so there should be no conflicts with Malwarebytes and Teatimer,as Malwarebytes free is basically a spyware scanner only.

I'm not 100% certain,but I believe the upgrade to Windows 7 might be equivalent to the Vista reinstall I listed above,if you decide on that.
There's an upgrade advisor available here:
http://windows.microsoft.com/upgradeadvisor
And some more info here:
http://windows.microsoft.com/upgrade