Generally speaking your project wouln't be that complicated. However, you certainly want to see your B-17 flying in a more or less compact formation. Therefore they should take off together in a row of at least three or four aircraft. That means you should add three or four invisible runways to the UK airfield and save each runway as separate ADE. The parkings should be as narrow to the runways as possible in order to really get the planes starting together. So far nothing impossible.
At Brest you also will add three or four invisible runways as waypoints.So far nothing special too, and it could look quite suitable. The only thing which could hurting you is the fact, that the B-17 approaching Brest will lower their gears. Unfortunately, and IMO, not a satisfying situation.
Bernard