Remember when running on utility power you will not have the voltage sags and surges you will see when running on a generator. Even relatively small loads that do not effect utility voltage when switched on or off will possibly have some impact on generator voltage. A 100 watt load is about 1.25% of capacity of a 8000 watt generator, it will result in a relatively small change in system voltage when switched, but think about how much smaller percentage of full load it is to a utility owned generator that puts out several megawatts of power, it will not be easy to measure any voltage change in the generator when switching such a small load.
Your clean power problems are because of the voltage fluctuations whenever load on the generator changes. That is why it was mentioned to isolate the pumps from the main controls, as the pumps will handle voltage fluctuations pretty well, but the controls will like to see more constant voltage. Something with battery backup and regulated to put out constant voltage will give greater results, and will not cost as much if it doesn't have to supply the pumps. A few hundred watts often makes a big difference in cost of this kind of equipment. Simple 12 volt inverter like is used for automotive and recreation will give you pretty clean power - if it doesn't have the surging motors, and if it is only driving the controls would not need to be very high of a capacity unit either. You still need something with battery if you can't have any loss of voltage even if it is only once when power transfers from utility to standby. If you can deal with getting past transfer then your options change some.
