Adebola put the Sky Blues ahead in the second minute, prodding home after a poor clearance from keeper Ben Foster
After a brief powercut in the stadium, Flood doubled the home lead 18 minutes later, firing in Marcus Hall's cross.
Six minutes after the restart, Ashley Young pulled a goal back for Watford but McSheffrey's 86th minute strike finally completed the win for Coventry.
Watford boss Adrian Boothroyd:
"We came out far too slowly in the first half. Coventry had a game plan and we simply didn't deal with it.
"The second half was different. We scored a great goal and had we nicked another I felt we could have won it, but we didn't manage to do that.
"You really have to be on your mettle in this division. You get punished for your mistakes and we need to learn that you can't play for 45 minutes or for an hour - it is a 95-minute game these days."
Coventry: Bywater, Duffy, Whing, Page, Hall, Flood (Jorgensen 72), Doyle, Hughes, McSheffrey (Impey 90), Adebola (Morrell 45), Scowcroft.
Subs Not Used: Ince, Watson.
Booked: Page, McSheffrey, Doyle.
Goals: Adebola 2, Flood 20, McSheffrey 86.
Watford: Foster, Chambers, Carlisle, Doyley, Stewart, Grant, Fletcher, Blizzard (Mahon 45), McNamee (Devlin 74), Young, Benjamin (Agbonlahor 45).
Subs Not Used: Chamberlain, Spring.
Booked: Stewart, Fletcher, Chambers, Foster.
Goals: Young 51.
Ref: Phil Joslin (Newark).