Once you have the entire frame stored in the AVR's RAM, its your discretion what you do with that frame. Send it over RS232 serial, or send it over bluetooth. Or send it over encapsulated UDP/TCP to another end.

Or convert it from LLAP to Ethertalk. Once you get the inside appletalk im sure it has ethertalk in it. But since AVRs are sorta slow, the best thing to do is receive the frame and hold up the bus until you get done processing, so the connected mac dont continue to talk until the bus is free. follow CSMA/CD to do this.

No you cannot use the PWM pins. Thats for output only. There are 2 ways to do this. You can either sample a datapin with a timer set for the proper bit timings but its MUUCH harder to synchronize. Easier to use the 2nd option, which is connect one of the data lines on an interrupt pin. such as INT0, or INT1. As long as you can set it to interrupt on both rising and falling transitions.

You still need the transceiver, as i dont think the data lines are 5V. They are 12V i believe.

This is frequency modulation FM0. or biphase, whatever the engineers call it these days. NOT pulse width modulation.