we're trying to make an android application that reads from a vehicles OBD-II port, but also has the ability to start the car, lock/unlock doors, window control etc.
Sounds like a illegal action in most countries.
If I understand correctly you want to make the following pipeline:
Android BT <---> BT Arduino < --> ELM327 <--> ODB-II
You could just connect - SparkFun OBD-II UART - WIG-09555 - SparkFun Electronics - with the Arduino using NewSoftSerial - NewSoftSerial | Arduiniana - remember that TX connects to RX and you need a common ground. I would certainly not make a separate PCB for that.
You have to search the forum for bluetooth Android side, no experience with that one. Keep us informed of your progress.