dwaive, the controller should not be getting hot. a few questions first.
Is this a short shuttle or a long run operation?
Does the battery loose more than 10% of it's 'at rest' voltage when the hydraulics are deadheaded? (if so, fix the battery problem before any further troubleshooting).
If the drive wheels are off the ground, can you turn both drive wheels by hand? (if not, fix the brakes or transmission problem first)
does this unit have any 'shorts to frame (check every power cable and fix any with less than 100K ohms short to frame before further troubleshooting)
On EV100 systems, I have found that if the wheels are free, and not dragging, but the panel is getting overly hot, especially if it is a long run and not short shuttle, I would replace or rebuild the 1a contactor. What can be happening is that the contactor pulls in, but does not make good contact, and because the recs keep pulsing, the driver is not aware that they are not really in bypass. this in turn does not allow the power to bypass the recs, so the recs never cool down, and are running full on.
I would also go over ever ALL the settings and reset all the settings to the factory specs.