unsure if I have cleaned all malware

I am not finding any malware in your logs. Just re-run Hitman and have it remove all those PUP's.

Any issues you may still be having should probably be addressed in the software forum.

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

1. We recommend you keep Malwarebytes Anti-Malware for scanning/removal of malware. You can uninstall RogueKiller and HitManPro.
2. Go back to step 4 of the READ ME and renable your Disk Emulation software with Defogger if you had disabled it.
3. Any other miscellaneous tools we may have had you install or download can be uninstalled and deleted.
4. If running Vista or Win 7, 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. Goto the C:\MGtools folder and find the MGclean.bat file. Double click on this file to run this cleanup program that will remove files and folders
   related to MGtools and some other items from our cleaning procedures.
7. After doing the above, you should work thru the below link
   
   • How to Protect yourself from malware!

Malware removal from a National Chain = $149
Malware removal from MajorGeeks = $0

 

No, it is not a problem.