Hey Robbie,
If you're keen to use the default CAN driver provided by libuavcan, you can specify any hardware timer that your application doesn't use, as described in the documentation. The driver supplied with libuavcan will configure the timer automatically, you don't need to worry about it.
The IRQ priority mask can be left unconfigured, the default is good enough for most use cases.
Concerning your questions:
2. Not sure I understand the question. What do you mean by inheriting functions? At any rate, rather than using the default driver, I advise you to implement an adapter class and use the Particle's default drivers.
Pavel.