OK, assuming this gplug timing is different than it used to be, I would:
1) Get a schematic for your model, that details the glow plug circuit. Post the schematic here if you can get one; that will help stir up more diagnostic comments.
2) Check the physical integrity of all the related wiring - harness, fuse holders, grounds, ignition switch. Take a close look at your battery terminals and cables. Any sign of corrosion or suspect connections, take apart, clean, re-assemble and coat with dielectric grease or your preference. I don't know what the implications of having a battery disconnected on your model are - I personally would be willing to disconnect a battery on a '99 tractor if it was mine, but don't want to create a false impression of knowledge I don't happen to have :laughing:.
3) Note on the schematic where the GP indicator light is being driven
from. If it is on the output side of the GP relay, then perhaps the relay is going south on you. Assuming that the GP relay is the lower cost item (compared to the control module) consider getting a relay to test with. I just bought 2 for my truck (it takes 2) to have as spares from Crank and Charge off Ebay. Not sure if they do Ag stuff, but their prices are good and they give you a warranty.
crank-n-charge on eBay
Nothing against OE, If Kubota's price is not crazy for a GPR, that's the way to go.
4) You need to be able to compare to another similar tractor, or get ON timing vs. temperature specs from a Service manual to really know if the control module/timer is working properly. If everything else checks out fine, and you still seem to be getting very narrow or inconsistent ON timing for the GPs, then you may need a new control module.
Rgds, D.