The common point between the two batteries IS supposed to be connected to the chassis, basically creating a 12 Volt (+) grounded system to half the lights and a (-) grounded 12 Volt system to the other half of the lights.
The generator, voltage regulator, and starter solenoid and starter are the only components that "see" 24 Volts, the fuel gauge and lighting loads "see" 12 Volts.
I've got a reply down another guy down on the DEERE Forum, and I'll cut and past a segment here...
"If you have an older model, there is a battery cable from the (+) terminal of the LH battery to the chassis, and a battery ground cable from the(-) terminal of the RH battery to chassis ground.
If it's been updated (for safety) or is above #90999, there's a common cable from the (+) terminal on the LH battery to the (-) terminal on the RH battery, and a slow-blow fuse in a jumper wire (or a length of fusible link wire) from that common connection to chassis ground.
If you have that system, with the crossover wire, that connection to the chassis MUST be present and intact for the lights, indicators and fuel gauge to function properly.
The (-) cable from the LH battery connects to the upper large terminal on the starter solenoid, from there a blue wire makes it's way through a circuit breaker (if new enough or updated) to the key switch and on to the light switch through some wiring harness connectors and a circuit breaker on the tip out steering pedestal panel... you should be "seeing" (-) 12 Volts (nominal) with respect to the chassis, on that blue wire both at the key switch and the light switch.
The (+) cable from the LH battery connects to the terminal on the starter "belly" facing the engine block, from there a brown wire makes it's way through a circuit breaker (if new enough or updated) to the key switch and on to the light switch through some wiring harness connectors and a circuit breaker on the tip out steering pedestal panel... you should be "seeing" (+) 12 Volts (nominal) with respect to the chassis, on that brown wire both at the key switch and the light switch.
If power is missing at the blue or brown wire at the light switch you'll need to trace it back through he breaker(s)on the tip-out panel, the wiring harness connector in that area, on through another harness connector under the rear of the hood/front of the steering pedestal cover, on down to the starter, though the pair of breakers there (if new enough or updated for safety.
So, check for the midpoint grounding of the batteries, and for the (+) 12 and (-) 12 Volts at the switch panel and let us know what you find! "
As to the SPARK when connecting the ground at the midpoint of the two batteries, the innards of the stater solenoid, the starter, the voltage regulator, and the generator need to be totally ISOLATED from their housings, frames, "bellies", etc, as any direct contact between a (+) 12 Volt part or a (-) 12 Volt part will cause the issue you are having.
Could be something connected wrong in the wiring, an internal short to the case/housing/frame of the components previously mentioned, a even POSSIBLE someone has installed a 12 Volt starter, or solenoid, or regulator, or generator NOT built with the internal isolation this system DEMANDS.
What is the serial number, and does it still have a generator or has it been converted to an alternator system?
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