In a case like this I would consider your operating system and any/all drives and network locations attached to it suspect. I'm surprised that WITH 3 trojans detected that a scan would even complete.
In this case if you have install software that you know isn't corrupt I would blow everything out and start over. If you save any of your personal information to a USB (etc.) consider all of it infected. I would consider the purchase of a good all around AV program, or at least setting Windows defense high, use UAC, etc. Doesn't really matter what you use as antivirus if you bypass it, so be careful what you click and download.
As to system performance AFTER you rectify the virus situation...get an SSD for your OS. Even a cheap one is going to far out perform your HDD.
I would look next to a GPU, based on your installed PSU.
Should be a pretty jam up box after that.