I see in the Tournament rules that pre-game initiative is decided randomly. Two questions based on this:
•Does this mean that the Knights of the Hollow Hill agenda has no effect until you have a plot card revealed? (This makes reasonable sense, since you aren't adding the "+2 Init" to anything)

•Does the pre-game initiative continue through pre-plot actions of the first plot, or is there another random decision after setup but before first plot?

Check out the Core Rule Book on p. 8. There, it talks about randomly choosing a "First Player" before houses and Agendas are formally announced and displayed to your opponent. So the +2 Init from KotHH is technically not even on the board when the set-up First Player is determined.

And yes - set-up First Player remains the First Player until the next determination of First Player takes place.

I never really though of this but does this mean that the first player would do his set up first and then the second player. Which would mean that if i was the second player, I would get to see the number of face down cards my oppent had laid for set up before i did my own set up?

Technically, yes. You could also choose which house you will have an Alliance with (if you're using that agenda) after you see which house your opponent is playing (if that matters at all).

Or decide exactly which chains you're going to put under your Maester's Path…