Have no idea why ATF wouldn't show on desktop in safe mode, it should. You can put it anywhere that is easy for you to find.
Those scans shouldn't take that long in safe mode as there is nothing to interfere with them running in safe mode. ATF will take no time at all.
The other two of course will take longer.
Just want to remind you that these trojans on your system do have the ability to "call home" and bring in more nasties. So the longer you wait the more infected your computer can become.
Whenever you get the time somebody will be here.