Thanks for the advice about correcting the generator problems. I thought that a buck-boost transformer might eliminate the problems with surges or low voltage occurrences but I didn't think about the harmonics problem. The motors of the pumps might eliminate some harmonics but the circuit boards are definitely seeing some kind of problem.
Do you know of any suppliers that would have a reasonably low cost protection for both the voltage variances and harmonic problems?

I'm not sure there is a MOV on the supply of the circuit boards. If rated correctly, this would eliminate spikes but not the harmonics. Maybe I could place a MOV at the buck-boost transformer, away from the gas pumps.