I found a manual for the EV-100 controller (note 10MB):
http://www.fsip.biz/Documents/EV100.pdf
Other manuals are available at:
http://www.fsip.biz/GEManualsDownload.html
It appears to be capable of 24-84V, so I agree that it would be best to use that, which would be much better than switching the batteries around for charging, as well as the problems that can occur with a parallel connection.
From what I have read of the manual, this controller is designed for a shunt wound motor (although it may also operate in series mode or separately excited mode) and incorporates forward and reverse as well as speed control by field weakening and PWM.
It may have other options such as seat switch, brake switch, plugging, top speed limit, auxiliary 24 VDC contactors, and
Regenerative Braking. The controller is usually pre-configured for the particular truck and motor(s) but there may be enough information to make the adjustments.
This controller actually uses SCRs for the PWM control. This is unusual for modern controllers, but it can be done by briefly reversing the current through the SCR by means of a pulse transformer, or by briefly bypassing the current by means of a capacitor, which appears to be the method used here. This is the first time I have seen such a controller so I am making some assumptions based on a brief overview of the schematic. The manual is very comprehensive and it is a rather impressive controller.