My Windows will not recognise flash drives or CDs when booted in normal mode, it only recognises them in Safe mode.
Who said you couldn't use Safe Mode? I have said Safe Mode with Networking several times.

I run it, it shows the expected dos box, says it's killing stuff please wait... after a couple of minutes the dos box disappears then pops up the Notepad with the log file. I assume that's success?
yes, that means it worked.

Then I tried mbam and it failed to start... does THAT mean the rkill did not work?
No, it means that the MBA-M file was not a new file downloaded AFTER rkill worked.

The steps must be done in a very specific way, if they cannot be done as written then posting back to say you could not do something would have been the way to go. If certain things do not work then very often there are other specific ways things should be done or other programs that could have been run in the place of those.
Your system is now obviously very damaged and the truly easiest thing for you to do is the full reformat and reinstall. There is no way now to be 100% certain that this infection has not "dug down so deep" that it will continue to plague you. It IS a personal information and password stealer so all of your personal files and information are at great risk. The quicker you do the reformat/reload the quicker you will be back up and running. But be sure you change all of your passwords and also notify any banks or credit card companies that you may have used online with this computer, all of those accounts are at risk.