I cut my ducting to accommodate the larger main tank & I use the full bypass, no problems with the gear doors & stock rams. I replaced the Pneumatic nose tire with a solid BVM one because it wouldn't fit in the bay once inflated. Mains are inflated to a max dia of 103 mm.
The Skymaster kit does need a bit of "tailoring" but it all comes together well & fly's very well. The landing gear is amazingly robust.
One thing you will notice is the Elevons, or Elevators are not level once you've made your first flights, there will be a very large maybe 3/8 inch difference on the right in a nose up direction, this is normal, I'm not sure if the wings are twisted or if the fuselage is twisted, but it seems to be there on many of them.