I'm playing in a PoTA game, 6 players, 3 familiars, 3 steeds, one sidekick. We're dealing with the fourth mega-baddie. Pretty sure the dm has upscaled it because we're 19th level. He interspersed Ghosts of Saltmarsh and another one involving the fey. I can't talk about the set up stories because they were blended in with the other adventures and I joined late, but before any of the main temples had been found.
So tips from a player:
I will be honest, figure out a way to not need to slog through a mega-dungeon unless you all love that play style. We took an oddball route and hit the temples one after another, then the Fain, then the mega-bads. It's been essentially 1 in-game day per zone, taking about 15-hours of play for each. (4 temples + 1 Fain + 4 baddies) x 15 hours = 135 hours. At our rate of play, that's taken us well over a year for what's an in-game week. your call if that is awesome or tedious. I find it tedious, YMMV.
Be aware the entire complex is designed to avoid calling reinforcements. Two active forges, multiple waterfalls, multiple lava-falls, "allies" who barely tolerate each other, numerous groups that fight internally, weird "sin" compulsions that make cultists ignore things they shouldn't, etc, etc, etc.
It means PCs can take rests almost at will because absolutely no one is going to notice anything is wrong. It's ludicrous to the extreme.
IMHO, restructure the physical layout, specifically the spaces between the published maps. I would put the 4 temples 1-3 miles apart with the "upper" level locations outside the mountain, with only the Fain and below underground.
Using the outside of the mountain also helps focus each cult in a different direction, possibly into multiple kingdoms. I'd have the water cult actually focus on an ocean reachable by a river from the mountain. That obscure the fact the are essentially neighbors.
Moving it outside the mountain means pillars of smoke, bolts of lightning and screams are more likely to be noticed, cutting down on the weird pacing, I think it should mean you can actually clear the zone with less play time because it becomes one long running fight, which means you don't need the same volume of enemies as a dozen set-piece fights
One advantage to this is that after the second cult, the PCs will likely figure out they can find other cultists if they circle the mountain. Let's you short circuit things. Alternately, the cults can notice their neighbor suffering from a case of "adventurers" and send "help". The kind of help that involves friendly fire.
It may even result in one cult being able to justify using their elemental doom bomb on another cult. A massove two-fer.