Assuming you have a decent battery in your transponder they will easily last six hours. I have taken out the transponders 24 hours after a club night and most of them are still flashing green.
BBK has a setting in it to allow you to assign multiple transponders to a team especially for endurance racing so you should be ok with your plan to use multiple transponders per team but I reckon you could just get away with using the one and whack the other handout in as a backup just incase it fails or starts flashing red.
I got excited when I read about you lot doing an endurance race. I am a big fan of endurance racing and myself and our team (Team shambles) have taken part and completed two 24 hour races, One in Belgium and one at York. I personally can't wait till the next EBOR at york because it was excellent fun and the challenge of getting one car to last a full event is brilliant.
Wheels and sticks? When running one car is quite easy to get round, just stick two receivers in the car and swap the plugs over, if you sort out a driving order so the wheel guys and the stick guys are driving after each other then swapping of plugs is minimised.
With regards to electrics well we have used the same speed controller and motor in both 24 hour races, neither were new when we first did one of these events and they are both still going today. In fact the 10.5 motor was used at the F2's last weekend and is still as strong as the day I brought it. I would advise using a connector and a adaptor to make sure you cannot conenct batteries up the wrong way.
Word of advice to race control, keep an eye on your spare transponder, we do a endurance race at our club every year, which nobody takes particularily seriously, One year out team had had a few failiures that put us back about twenty laps to the leaders, so one of snuck into race control, snaffled the second transponder and we stuck it into a spare car and whacked it on track, making sure that the car was circulating 10 seconds apart from the main car we soon made up the defecit
We got told off an penalised but it was bloddy funny watching the team of club hotshots trying to work out how we had got five laps in front of them in under 10 minutes.
Look forward to hearing more about this event.