questions before following instructions in the Malware Removal Guide

Over at the Software forum (see my thread "suddenly lost an application; plus, can't download anything" at http://forums.majorgeeks.com/showthread.php?t=286066), Administrator DavidGP recommended I follow the instructions in the Malware Removal Guide and then start a new thread here in the Malware Forum.

But I have to ask three questions before I can follow those instructions. I'm sorry if I'm posting these questions in the wrong forum, but I asked the first two of these questions over at the Software forum, but didn't get a response.

A little background: My brother's computer runs Windows 7 Professional with Service Pack 1, and Mozilla Firefox 29.0.1. His current security software is StopZilla AVM 2013 (product version: 6.0.0.0, file version 6.0.3.61), and of course Windows Defender and Windows Firewall.

Question 1:

Both StopZilla and Windows Defender run real-time protection, but somehow don't collide with each other.

Nonetheless, I guess I'll have to uninstall StopZilla in order to run the programs referenced in the Malware Removal Guide, rather than just disable it, right?

(Incidentally, full scans done by both StopZilla and Defender found no threat.)

Question 2:

Step 4 of MajorGeeks' Malware Removal Guide says to disable any disk emulation software.

I don't know anything about disk emulation software, but I can tell you this:

My brother was running the now mysteriously disappeared program (FloorPlan 3D) under Windows XP Professional, since FloorPlan 3D is an old program that won't run under his OS, Windows 7. In order to make that work, he ran Windows XP on a virtual machine created by Oracle VM VirtualBox Manager (version 4.2.14). Therefore, Windows XP appears to be running on virtual drive Z.

Is VirtualBox disk emulation software? If so, I can disable it with DeFogger.

Question 3:

Someone told me they thought it might not be a good idea to disable disk emulation software before running diagnostic software because the malware might be on an emulated drive. Any comments on this?

Thanks for any help anyone can give.