There seems to be an issue with the beginning of the first iteration.
After a complete session is done (until the last extension in the dialog was disabled), half of my extensions are still enabled in FFs add-on manager. I guess the first iteration did not correctly register them. From 82 installed extension only 31 ever show up as "suspect".
Also, the "Continue" button appears to do nothing at all for the first iteration, and "Start a new session" is still enabled in the menu, while "Continue... " is not. But session info shows a new session with ID. No extensions are disabled, and only after a manual restart I can start with "Continue with next iteration". A feedback would be useful here, and a protection against >1 running sessions.
Other observations:
If the "FECT Progress Report" tab is left open at a restart it does not update. An updated version must manually be created from the menu.
Progress report says "Iteration: [N] :Conflict was resolved" when for resolved "No" was clicked.
End session should be automatic if nothing is left to do.
FECT info says "It will randomly disable/enable one half of the installed extensions during each iteration". I have not checked if FECT really works so, but why randomly? Strictly by alphabet would allow the curious user to follow and understand the procedure. (IIRC, the old did it this way and it was comforting to see the logic at work.
Other Suggestions:
The sound effects are very annoying (at least to me). Allow us to turn them off.
Have a pop-up or new tab open after every restart; to automatically notify that a session is still open. Also, progress report could go there, and the content of the "continue session" dialog could be conveniently accessible from/in there.
Make it possible to start without defining a broken extension. This way, FECT could be used to track other unwanted extension effects ("Who killed my animated GIFs?!!?").
Give FECT additional menu entries to disable/enable all extensions for manual testing outside sesssions. I have found that FF behaved differently after a FF restart with disabled add-ons and after a restart after manually (tediously) disabling all extensions. Such a menu would be so useful to check for these cases!
Many points, but still, I'm impressed with this functionality in an alpha!