My oppinion... Absolutely not!
I repaired the frame on a mid 60's 1/2 ton that was notched the same way to clear some exhaust manifolds. When the truck cam into the shop the whole front end was about ready to fall off. Those small notches had invited substantial cracks running top to bottom of the frame rails, both sides. The owner was very lucky it did not fall apart on the way to the shop, and I was hesitant to put it on the lift for fear the whole front end would fall off.
As part of the repair I replaced the portions of the frame that were missing (the same parts you are considering removing, or have already started) oddly enough they were not at all in the way on that truck.
I have seen what removing portions of the frame flanges leads to, don't take that risk.
Even with some sort of strengthening I don't think it is a good idea, particularly on a heavy truck with a substantial engine sitting in there.
What other options do you have? can you make headers to go outside the frame? or up through the hood? Or manifolds that exit forward then the exhaust pipe turns back? A different engine? Hopefully there is a safer way to accomplish your goal.
Grigg