Hmm, for this one I think you should stick with a single age (with multiple temple buildings) and ground it in solid-ish quasi-physics. (Given that I myself am considering an outright stupid mumbo-jumbo multiple age RGB thing with my AP shell, that would make me a hypocrite :P).
I hate puzzles that involves time in RL impractical or stressful manners, but with the Mayans so known for their astronomy and calendars (for all that your age concept is mostly about the architecture), it would seem neat to let one aspect of the puzzle be the figuring out, directly between which of a couple of mountain peaks a sun will rise alone and unoccluded, when it will rise and which spot would make for the best vantage point. If we are to create the mist by artificial means, on such a large scale, might it make sense to use the surrounding nature somehow? Maybe make the temples gigantic fountains, which can soak the hills around them with water, that will vapourise at dawn. Connect these with a huge scale high pressure pipe system and you have possibilites for another set of puzzles, as well as speedy transportation between the temples, in pods inside the pipes. Water supply would only suffice to a single full rainbow "summoning" per day, to make it harder to come up with the right answer(s) by chance.
Perhaps you could have a few suns/(reflective)planets with different spectral profiles, so that each could produce a rainbow, with certain characteristics -- you just need to figure out when they rise or set alone. I could see the creators of the system giving names to each of these rainbows and the locations in which they appear, maybe simply something translating to Daughter_of_Name-of-sun, Son_o_Name-of-valley.
Hmm, one special case when you could get several simultaneous individual rainbows in cardinal directions (because that day all suns/planets rise/set simultaneously, set far apart along the horizon), could be cool and have been a special holiday historically, but that would take overcoming the suggested water supply limitation.
Hope there's something in there... :7