I powder coat my pumps. I disassembly the entire frame and have all the individual pieces sandblasted and then powder coated. Then I reassemble them with all hardware (nuts, bolts & washers).
I don't like the idea of leaving the frames together as you still have dirt & rust between all the mating surfaces...I wouldn't be able to sleep knowing that I took a short cut...but that's just me...I don't sleep much anyways...no time to be laying in bed.
Here's a few photo's of a MS80 I working on currently. In the 2nd photo I just finished reataching the upright frame rails to the base. Then installed the top brace.
At the end of day, it's your pump and the only right way to do it is your own way. Enjoy.