tigerdude426 - here's what I did to ensure those inside root ribs were flush against the fuselage. Built both wing halves but left the inner ply root rib off. Built the fuselage. Glued on one ply root rib at a time.... to do this, install your wing tube and dowel in the fuselage and then punch holes in a piece of wax paper and place this on the first side you're gluing the rib(will keep any glue from getting on the fuselage). Put glue on the face of the root rib and mount root rib on the wing. Quickly mount this wing on the fuselage and then put the other wing on(no glue). Stand the plane on end and put a little weight on the top wing to hold the wing flush against the fuselage. Next, insert toothpicks where there is a gap between the fuselage and the root rib to flex the rib towards the fuselage to close this gap. Wick in ambroid glue or thick CA to act as a filler to hold this position. Once the glue dries the root rib will be flush against the fuselage. Repeat for other wing half. Fill the rest of the gaps as required with filler.
Post in my SSE build thread.
In your case, you could build another root rib and install it in this fashion. Don't imagine it would mess with the plane's characteristics much.
Hope this helps.
somegeek