Just playing around looking at it and reading the .pdf file.
Awesome piece of work!
I presume I can start the ME before I start WOFF?
Yes, you can start it anytime, ie. either prior to launch of WOFF UE or when the ME window in the WOFF pops up.
And the readme says to "close" ME after I make any changes to a campaign mission
Yes, save your changes and close Mission Editor. It must be restarted for the next mission to enable Open Mission file menu.
Guess I have two questions: The .pdf also states that I can alter the skill and morale of flight members.
I don't necessarily see myself using this but it's a nice option for campaign quirks and to better understand ME.
Are these changes permanent or just for that flight?
Only for this edited mission. For the next mission it returns to WOFF campaign settings.