The problem isn't so much the direction of retraction, the real problem is getting the gear spaced far enough apart that it's got a nice wide track for better ground handling, particularly on grass. Once you get it spread out far enough for that, if it's mounted in the fuse, you need to make sure the fuse is wide enough to house the flaps as well.
Keep in mind that on a 55" span (such as this one) By the time you get a minimal distance between the gear, say 16" even (which is narrow, but probably close to what the small F16's are) you are already down to a 19.5" wing panel, that doesn't leave much room for an aileron AND flap. But if the fuse section is say 30" wide, with 12.5" wing panels (which seems a little silly I know, but it's really not THAT much shorter than the small F16's again, you can have a 12" aileron and a 12" flap. And really a 30" wide fuse section isn't that bad. It may not need to be that wide, but we haven't gotten that far with the drawings. I think if it was somewhere between 24 and 30" wide that would be the best, gear could retract normally, flaps would fit in the fuse section, and it will all remain strong with nice integral formers through the fuse

As for the bigger one, with the bigger engines it's quite possible that the engine could move forward. I'll talk with Stefan about that. But keep in mind, even with the bigger engine further back, the nose gets that much longer and heavier. I think it would still balance ok, it has a very long nose moment