Wow, this sounds like a fun one!
Let's try a different approach. Let's see if we can determine why you've had an ongoing 'overcharging of your batteries' issue, that seems to still be happening, correct?
Give us the battery voltage present with the tractor running, by reading across the battery posts, NOT the cable ends attached to the battery.
Give us some history on your tractor too. How many hours on it, and how recently did you install the new v-reg and alternator, and battery. Were all replaced items new from Kioti, (except battery)? What brand and rating on the new battery?
And, what condition are the battery ends, at both the battery and at the location where the ground cable attaches to the frame/chassis?
What is the condition of the wires at the starter, hot and other wires. What is the condition at the fuse box and it's fuses. Is there any corrosion anywhere in the paths I've mentioned.
Are there any loose connections anywhere above?
After answering the above questions run a jumper cable (from a pair of heavy duty jumper cables) from the negative battery post down to a bare metal ground on the tractor. Do this from the negative post of the battery, with the normal ground cable disconnected, temporarily. If the problem goes away, your negative ground cable is bad and not grounding your battery properly. This type of problem with a bad cable can also happen on the positive side of the battery. We'll get to that later if needed.