Ok, I don't have a MEP-002 or MEP-003 so don't feel qualified to offer advice on their quirks. I can say that my MEP-701a is well within the accepted 58-62 hz tolerance range for home standby generators when it comes to setting the throttle position and forgetting it, with about a 1 hz typical load swing, plus about +/-1 hz hot or cold. As to the cheap "automatic" transfer switches typically bundled with Generac Guardian home standby generators there is a reason they are cheap, namely they are braindead and are not real automatic switches, instead the computer in the generator control board controls their operation. So without a compatible Generac brand generator they are nothing but a paperweight (basically a switch with a servo mechanism).
Other problems that I see is the fact these J series Onan diesel engines (like in the MEP-002 and MEP-003) are notorious for being hard to start in cold/cool weather, and require a lot of time with the glow plugs/heaters on. Given your north Florida location you could probably get around that with the addition of a magnetic oil pan heater that could be ran in the cooler months (I am not sure if it is worth it though, as this would likely consume $20+ of electricity per month).
Having said all this, if it were me and if this is something that had to work, I would remove the entire original control system and install something like a Flight Systems #540 controller (if you call and explain your situation they will often work with you on pricing, give you dealer pricing, etc) As to the need for possibly reflash the field, I think Power Tronics makes an automatic field flasher AFM-500X module that might be able to be wired in with the existing voltage regulator, even though it is designed to work with their house branded AVR's.
Ike
p.s. it really is not that hard to start a generator and flip a manual transfer switch, if someone can start a car and put it in gear, they can start one of these MEP generators and flip a manual transfer switch. If your decide to look at a whole house manual transfer switch that does not cost too much money, I suggest looking at the Ronk brand units, they are reasonably priced, come in an aluminum NEMA 3R housing , and my 70+ year old mother can easily flip the spring loaded lever on their 400 amp box. Due to the relatively complexity of starting a MEP generator I opted for a surplus commercial Kohler unit for my mother's house after my step father died a couple of years ago (their old generator was a 6500 watt pull start Honda) , now to start it all she has to do is flip a light switch style remote start switch, give it a few seconds to crank and warm up, then flip the transfer switch.
