So, as pointed out by BlacklightVoid, there was a bug with the new BFG aiming that prevented it from shooting at certain inclines. This was basically my fault for making an assumption about how the math worked out. I've now fixed that, and also made it less likely to clip the floor or ceiling with shots over/under ledges (still not perfect, seems impossible to be perfect at this but it's pretty good). 

Also, there is now a Scythe 2 patch in the Addons and Patches zip. Any wad with custom monsters will need one of these with the main mod due to how the logic inside works, but they're not overly hard to make.

Anyhow, this whole BFG business has made me think that maybe just rewriting how the weapon works a bit under the hood might be worth it, so there may be another update soon-ish if I can figure out a better method for doing what I want to do. If only GZDoom would just let me clip projectiles through floors and ceilings I'd just do that, but sadly it's not possible :^(