The flap tube comes with flap handle positions for the normal (lef side) and the Sport Trainer (center) versions. Since I'm making the standard version, the attach angle for the center flap handle is in the way and needs to be removed.
I started cutting this down with a hacksaw, then fine-tuned the angle with a Dremel tool with a metal cutting wheel. This gave very good results, and enabled me to get very close to the angle welds without cutting into them (the factory told me the welds need to remain intact for structural integrity of the tube).
I then taped off and sprayed the resulting bare metal with NAPA 7220 self-etching primer, then a coat of Rustoleum rust preventative semi-gloss black paint, and two coats of Rustoleum automotive clear coat. It won't be as good a covering as the original powder coat, but it should be sufficient to prevent corrosion and look decent.