I like your plan. I assume there are drain holes to remove any water from rinsing. be sure they remain open and clear with any treatment you do.
I had a front fender chemically striped. The company didn't have any rust inhibitor treatment process so i took 2 part epoxy paint, taped the edges of the back side brace and poured the paint in and sloshed it around till i felt it was fully coated, then drained. Seemed to work well.
