This is all based on experience from last year (on a couple of coaster-centric trips)...
We generally hit Manta first for 2-3 rides, then Kraken for 2-3 rides. They were opening the part of the park with Mako an hour or so later than the front of the park when we went, so we would time riding it for that. (They had a literal rope drop back there, right at the Spice Mill restaurant.)
I'm not sure where that would put you with the shows. You may want to do one or even two (dolphins, pets and/or sea lions) between Kraken and Mako to avoid too much backtracking. It really depends on the show times and what you really want to see. If you do a show or two before Mako, the line will be longer, but I don't think the line builds too early, and it's a pretty fast loader. We always hit it before shows since it is our favorite, and we love to ride it over and over. I think we did 10 rides our first trip. On Kraken and Mako, we have had times when there were so few people in line after our first ride or two that we got to just stay on. It was pretty awesome.