Looking very good. When I installed my LQ4 I found that the stock exhaust (including manifolds) from my donor cleared everything with just a slight adjustment to a hanger near the aforementioned crossmember. You have headers so your situation is different. Those cross members do not have much section height to begin with so I would caution you on notching the stock member. If I had to I would add a hoop to bolt on over the top of exhaust pipe to keep everything rigid. Looks like you are more than capable of figuring it out, so please share your eventual solution.
Yes, not really a fan of notching the stock crossmember. Right now I'm thinking of two possible fabrication solutions for a custom transmission crossmember.
1) I measured the space between the floor of the cab and the top of the frame on my stock running '96 C1500 RCLB and found it to be about 1.25". I could fabricate a member that hangs from the top of the frame and drops down in the center to support the transmission. (Sort of a V with wings)
2) Fabricate a crossmember that sits on the bottom lip of the frame, angles up and over the exhaust tubes then down under the transmission tailshaft back up over the second tube and back down to the opposite fame.
I am lowering the truck so I am reluctant to go below the bottom lip of the frame as I don't want something hanging down to cause an unexpected driving event later on.