Hi,
T=0 and T=1 are quite similar, and I don't know if any adjustment is required on the firmware. Maybe the firmware only needs to tell the micro-controller to switch to T=1, and then it works flawlessly. Harald Welte would be able to answer this question in more details, but he is not online before next week.
Mmm, although they are similar at the higer levels, T=0 and T=1 are pretty different at the 'byte' level and I'm pretty sure you'll need to adapt both the firmware and the host app (since it tries to interpret the bytes to fw entire APDU to wireshark).
Cheers,
Sylvain