Okay, so I have played a solo-ish game to learn rules, then two two-player games to familiarize my friends with the game (by the way, works very well because explaining eats a lot of time and the game does take that long, and neither time have we even finished the first week). After these experiences, I have a couple questions for now:

1. How many TESTIMONY lead markers are placed on the board? All, or just "suspects +1" = to the amount of players?

2. My friend really wanted to kill Floyd's Father Michael NPC so he could use certain dark cards against me. Can an NPC be assassinated or does that only happen to suspects? How do you kill an NPC besides plot, or is that the only time an NPC can be killed? I don't know if he had a bad shuffle or what but it seemed a decent amount of dark cards were dependent on the Father's death.

You only place the testimony leads corresponding to the active suspects in the game, so yeah, just suspects +1

NPC elimination mostly occurs only as a result of plot; the only exception I can think of is Tanaka, whom Louis can kill in a Fight. It's definitely not possible for another player to kill them. It might indeed have been a bad shuffle; I know there are at least some dark cards that need Father Michael to be alive instead, but one might regard being made vulnerable to certain dark cards (but not others) as a cost of choosing the "Uphold your first directive" plot branch. Either way, it's often the case that one will draw certain dark cards that one probably won't ever be able to play; the best thing to do is just discard them to reduce the cost of another card.