So you got away from notching the frame by raising the Atlas up above it? And with no body lift, you are cutting a significant amount of the tunnel and floor board?
The double boots I got from Atlas promptly cracked. I haven't fixed that yet, but perhaps two singles would work better?
My biggest issue is rear driveline angle, so I ended up with a flange at the T-case down to a 1310 at the axle. It works, but I know if the whole axle droops, I am near it's limits. Someday, I will move the rear back a few inches to help alleviate this. But the flat belly was well worth it!!