Could you please post more information on hardware setup?
Header layout depends on the logic analyzer though Mictor is a somewhat common connector.
Other than a complete port, a spare SPI may be fast enough and may be preferred as SPI can be the source or sink of biphase (clock recovery from one signal as signal is data plus clock)
Is there any way of accessing any breakpoints in AVR?
In linked article, Atmel Studio has been replaced by Microchip Studio.
[page 5, package lower right corner]
Pinout AT90CAN32/64/128 - TQFP
Getting Started with Configurable Custom Logic (CCL) (mid-page for bi-phase)
[page 19, middle of left column]
14.7.10 Biphase coding1041
A biphase encoder and decoder can be in a sPLD.
Microchip Studio (operator's manual)