I see a lot of this as I work a lot with generators supplying rectifiers and UPS systems. Affraid most of your problems lay in the design/planning or lack of it. I doubt there will be an inexpensive fix
Ron hit on some of the deatails, especially the generator rating versus the measured load rating. When a UPS is involved you need to be at a 2:1 ratio.
Fist step to do is balance the load evenly accross all phases.
If that does not work then the next step is to have a UPS designed to work with a generator, that has built-in or add on filtering, and a sensor input to tell the UPS when going on generator to "Walk-In" the rectifiers.
