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Faunsdale, AL | OK, just to make sure. You have a 24 volt tractor with a generator and 2 12 volt batteries. Some later tractors had a single cross over cable under the floor plate that connected the batteries, but I believe the factory design for the 4010 was always to have each battery connected to the bolts on the cover of the transmission by a short cable. In effect half of the tractor's accessory circuits (lights and gauges etc.) operate on 12 volts positive ground (off left battery) and half operate on 12 volts negative ground (off right battery) while the generator and starter use and deliver 24 volts (actually ~28 volts DC). The starter and the generator should both operate isolated from ground and only closed into the 24 volt circuit when the starter solenoid closes while cranking in the case of the starter and when the regulator cutout closes in the case of the generator.
If it cranked up when you installed the batteries, and the gen light went out when you sped up the engine, I assume it was connected up correctly. What may be wrong is the regulator cutout is bad or the generator to regulator wiring is incorrect etc so the generator is killing the batteries when it's not charging. You need to charge the batteries separately and then check the voltage on the batteries (both of them, check from starter solenoid terminal where the battery cable connects to the terminal on the back side of the starter casing where the battery cable from the right battery connects or even the stud that the starter solenoid is strapped to. You should have battery voltage (24-25 volts) with the engine stopped and this should increase to 27.5-29.5 volts as you speed up the engine and the batteries charge up.
If that is all functional, then the most common reason for the tractor to be dead in the morning is a short from brush dust etc in the starter motor. The right battery would be the dead one in this case. If both batteries are dead, then suspect the generator and regulator. Other small loads like lights and gauges could kill both batteries if the switch is left on or is wired up incorrectly.
Any time you install batteries, regulator or generator in a machine, you should probably polarize the generator by shorting from the regulator BAT terminal to the GEN terminal next to it. Just a spark is all that is needed to restore the magnetic field in the generator iron that it uses to build up voltage so that the regulator cutout will close and connect the generator output to the electrical system/batteries. When the engine slows down or stops, the cutout should open to prevent the batteries from discharging through the generator. This does not prevent one battery on your tractor from being discharged through a defective generator even if the cutout functions properly.
Here's a link to some really good PDF's of the diagrams
http://www.geocities.com/gwece/deere/
One mistake I noticed is on the PDF file 4010wiredia1, the regulator terminal marked GND at the top is NOT a ground! It is shown connected to the brown wire from the generator A2 terminal and goes on to the terminal on the starter that is connected to the right battery POS post. Definitely not a ground!
And here's a scan you can look at as well
Edited by ccjersey 3/17/2012 22:37
 (2011-07-09_171949_john_deere_4010_wiring.jpg)
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 2011-07-09_171949_john_deere_4010_wiring.jpg (60KB - 1482 downloads)
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JD 4010 batterys
