Hi,
port T is the best solution because it is a timer input. It provides you a possibility to measure pulse length to get required info about input. You do not care about frequency of the input pulses if the information carrier is absolute value of the pulse length.
If it is a manchester (NRZ) I do not know what is signal coding. If it is still pulse length then you can use, for example, external RS232 transceiver to change NRZ to (0;5)V. Such transformed pulse can be then connected to timer input capture pin to measure length of the pulse or to another input pin which is able to recognize input protocol (if any).
The same is valid in opposite direction just another timer pin is used in a output compare mode to generate proper pulse length or you can use some of the PortP pins if you want to use PWM output to generate pulse of defined frequency and pulse length. Also RS232 can transform (0;5)V signal to manchester NRZ format.
Best regards,
Ladislav