What might be the case is that different chemistry have slightly different voltages. I.E, what we call a "36v" LiPo is slightly different than a 36v SLA battery, so the throttle would need to have a slightly differently calibrated sensor. I doubt it makes a big difference, though. I do know that when I went from 36v to 48v my 36v throttle didn't work perfectly anymore (big jumps do matter).
Sorry I can't help you with the controller. Looking at how PAS systems work, there are multiple different systems (both PAS systems that output a throttle signal, and those that simply output a signal proportional to your pedaling, and if above a threshold, allow the motor to engage).
In your system you seem to indicate that it has a throttle and a PAS system. So it might work to short the PAS wires on the controller side (like you suggested) if the system is passive. Alternatively if the wiring needs an active power source [PAS system is generating minuscule power], then I guess shorting the wires wont work. I can't think of any reason it would be bad to try, though.
But, in general, if you want help on the forums you need to lay out what you have, what you're trying to do, what you're saying, etc, more clearly. Even your last post is really kind of stream-of-conscious. I'm probably only noticing this because I have a bad tendency to do it as well.
