1. If I remember correctly in one of the novels, during Tyrion's Joffrey trial, people were called as witnesses. I cannot remember who served on the jury but I remember the deck being stacked against him. How many NPC's should I have on the jury? Should I just have random citizens or the accusers serve on the jury? I can't remember how GRRM wrote that in to the books.
Feudalism knows no 'jury of ones peers'. Lowborn characters, even minor nobles are judged by whoever holds the right of pits and gallows on the land where they committed their crimes. High-born lords who hold the right to judge themselves get a 'jury of their peers' but on that is not subject to strict rules, but rather everybody that can be convinced to join the process and share responsibility by the party bringing the accusations or by the defence.
2. In the case of the examination where a "lawyer" would be cross-examining the PC's, what would be the best way to run the Intrigue? The PC's would be trying to convince a jury, not the lawyer "cross-examining". I was planning on treating the trial as a Complex Intrigue, but I was hoping for some advice/recommendations on how to run it.
There might not even be a cross-examination allowed.
All the usual tricks lawyers pull today, especially in the US, would probably grounds for a duel of honor or for being tossed out of court outright.
Most of the work of showing the character to be innocent would probably have to be done by intrigue and behind-the-scenes maneuvering if you do not dare to risk decision by combat.