I have experienced the same issues with fitting the wheel wells, but only on the starboard wing. Glued the walls to the upper wings, using the recesses and edges as a guide, and when it came to (dry)fit the wings, the starboard upper wing is approximately 1 mm further inboard than the lower wing. The reason for doing so is that the joins will be more visible on the upper wing than the lower wing.
The wheel well walls now fit snugly against the ribs and stringers of the upper wings, and when I align the upper and lower wings so that the panel lines between upper and lower match exactly, one wheel well is 1 mm further inboard. If I assembled the wheel wells according to the instructions, would not the upper and lower wings then match up?
Also I find that the bulkheads forward and aft of the cockpit need some sanding to reduce their widths as they will put pressure on the wheel wells and push the wings out so the inner wings end up with an anhedral whereas the inner section should be flat.
Edited by jenshb, 15 December 2017 - 10:55 PM.