Software programs not running as they should

Hello,
I come from the malware section of the forum. I recently was infected with a malware problem but since have solved the problem (I hope). Now the remnants of the malware has left me with semi-functioning software issues. For instance, I am unable to use my all in one printer/scanner, I cannot backup my iPhone to iTunes, MS Word is glitchy and throws error codes when I open it, and last but not least, I cant save HiJackThis logs to my computer. The best I can do is save screenshots and post them as pictures. Help!

Computer:
Custom build
Windows 7 Professional x64 Service Pack 1
AMD Phenom II X6 1090T Processor running at 3.2 GHz
8GB Ram
NVIDIA GeForce GTS 450
160GB Corsair SSD (Runs OS)
1TB Seagate HDD

 

Words like "cant" and "unable" are very difficult to understand. Please explain what happens when you are trying to do what.