Going to start CW on Imperial side, which misc quests should be done that can't be done after the Imps win? I know "Missing in Action" in Whiterun is one, are there any others?

I always thought Missing in Action could be completed regardless of what side you chose.

Shame you can't take the option Tullius should have given you.

I was able to complete Missing In Action after the Imperial Civil War questline. As far as I know, no major quests get blocked out as a result of the war.