Hey, Jim....
There's a way to get (some) cleanup done before you run the apps to get rid of malware/etc.
Create a third-party app called C-Cleaner.
Point it to:
http://www.piriform.com/ccleaner/downlo ... wnloadfile
Download file: %ThirdParty%\ccslim.exe
Command 1: %ThirdParty%\ccslim.exe /S
(this does a silent install of cc-slim, which doesn't include bundleware)
Command 2: C:\Program Files\CCleaner\CCleaner64.exe /AUTO
(automatic cleaning routine begins - use the 64-bit radial button)
Command 3: C:\Program Files\CCleaner\CCleaner.exe /AUTO
(same thing, except 32-bit)
Now, make this your top third party program.
Add other third-party programs as desired - as discussed earlier in the thread, you can actually add the built-in apps to your third party list by referring to them by name, and the automation features will still work. In this manner, you use CCleaner to kill the junk files first, and then can run rkill, tdss, mbam, etc, in the order you like.
If that doesn't appeal, look at the scripting possibilities. Everything in the system repair section (and beyond) is a scripting option.
My only question for Fred on this one is... is there a way to call the apps in a Script that would keep the automation routines in place?
What a user could do is set the script up to run individual fixes (rather than groups) in any order he or she chose, while calling on UVK to run the automatic download/install/run routines for the built-ins.
I'm thinking <run_malwarebytes> or something that would just act as if the checkbox were ticked.