Can I re-cut the angle on the underside of the boom without screwing everything up (Tail boom to fuse strut and overall length of tail to wing)?
While I haven't looked at the model, I think cutting the boom's angle will shorten the boom and throw the proportions off. You'll have to ADD a spliced section to the boom to decrease that joint angle, not cut anything away. I'll go take a look at the model & perhaps have more advice once I've seen it.
OK - I just looked at the model - here's what I'd do: 1. Do NOT cut any angle off the wing end of the boom - cut 'em square. 2. Notch the wing upper surface to accommodate the blunt boom end as an inset that will glue to the inside bottom surface of the wing. 3. Use a watercolor pen to silver in any exposed paper.
Hope that helps (I don't see how the prototype got built any other way than what I just described, because as drawn the booms would stick up like porcupine quills - as you discovered!)