I finally had a chance to run the published version of TC. I have read the comments and concerns and am posting this as a general list of things you could do to fit it in to a four hour slot.
A few notes on the table I ran: My round ran four hours with an extra ten-fifteen minutes for end of game paper work. Tier 1. PC's had a fair amount of appropriate skills spread over three of them (Know: Nature, Know: Religion, Perception, Linguistics, Diplomacy). PC's had the capability to use Speak with Plants but did not cast the spell once. PC's never went to the weavers house, never went to the artisans square and never even saw the children. That being said they figured out most of the town's secrets from the Sheriff, the head priest, the journal, role playing speculation with each other (and Nira) and the cloaker's performance. They had the optional encounter and killed the cloaker. PC's saved Nira and returned the artifact to the PFS (but felt really bed about the fate of Mercy without the artifact).
The first thing I would advise is to not stress out (as a DM) that PC's MUST obtain every last scrap of knowledge contained within the scenario. For some the investigation will go their way and for some it will not and that will frustrate some players but that's just the way it is. I know conventional wisdom claims a scenario supply ALL motivation, background and secrets within it's short run time so that no one goes home feeling unsatisfied but TC is simply not that kind of scenario. And not all scenarios are designed for all mixture of characters or all players. And that's okay.
I don't think there is any harm in letting a table of players know TC is a skill heavy investigation and they might want to have an appropriate mixture of character classes. If they chose to bring six city slicker hack and slash warriors then so be it.
There are multiple ways to get enough information to figure out what is happening. There appears to be common concern a party lacking Know: Nature and / or the ability to cast Speak with Plants is SOL but as I pointed out above, my table never bothered to use Speak with Plants and never even saw the children and managed to succeed in the primary and most secondary victory conditions.
Specific Tips (not previously mentioned in the thread):
Use the journal to quickly supply them with information they are missing. As written in TC Amenira's journal is used to supply the PC's with a clue on how to interact with the town folk. It can also be used to house all manner of additional information. More about the Smiling Shadow of Flight, more about Azathoth, more about the town, more about the investigation , more about the sheriff, etc. You can quickly sum up information and point them exactly where you need them to be. My table obsessed over the journal, spent hours reading it and then marched to the Sheriff for more answers.
Use the cloakers performance (see previous post earlier in thread) for more information about the cloaker.
Use Nira to point them in the right direct. Remember, Nira is Amenira. You can have Nira offer flashes of coherence and give advice or answers. She can lead PC's away from Red Herrings and point them on the correct path. She can be as cryptic and awkward (or not) as you see fit to use her.
Finally: Condense the Impossible Forest!
Too many caves to explore! Ugh.
There is no reason the Impossible Forest can't be one large cave. Any reasonable plan will find the Verdant Spark. Detect Magic will find it quicker.
If you want to keep a hidden treasure cave have it near the entrance. OR you can combine the hidden treasure cave with Sheriff Molume's gifts. When he hands over the "This might help you beat the monster" loot he can add the potions saying, "A visiting alchemist gave us these for payment but we have not the means to know what they are".
If you have time for the optional encounter, try to stage it after PC's are leaving the Impossible Forest and exiting the crevice. That seems like more reasonable placement.
I had the cloaker circling above the crevice when PC emerged. It was deciding if it could kill three of them (or not). It dive bombed them when Nira popped out of a PC backpack.
Anyway, even if the PC's are out of time for the actual combat they can come out, see it, it flies away, they shoot after it and maybe get an arrow or magic missile in. Which leads to...
Later they find the cloaker "riddled with bullet holes" on the side of the road, then you can throw in that the damage PC's did to it was instrumental in helping take it down.
Partial closure.
Also, a very broad tip that may be common sense for a DM but ...
I've always found Living campaign modules to be a blue print of the most likely way to tackle that particular story but you should never feel as if your hands are tied to do it exactly as the scenario says. The scenario doesn't know you, your players or their class combination so when the modules says, "Players must have Skill A or B" or they get zero information, take it with a grain of salt.
Despite my insistence that it's okay if players don't get all the answers in TC that is a far cry from getting zero answers and then thrusting PC's in to the Impossible Forest for the final encounter.
Feel free to reward players for good role playing, or hell, for just having fun.
For example:
If you have a table with no appropriate skills and no way to cast Speak With Plants just pick a random (appropriate) PC's and start telling them things like, "When you were a kid, you remember your mother working daily in the garden. You were more of an eater than a grower so never helped out but you would swear she always said that vegetable A and vegetable B don't grow together because they'll produce rot and wipe out the entire crop. But that garden over there is growing both of them and they look healthy. Weird."
In the case of TC feel free to hand the PC's a few bits of free information if you think it will enhance their story telling experience. The only loose rule I would add to that is don't let the substance of said free information out weight the substance of information PC's work for.
Free information should be just enough crumbs to keep them from starving. =)
In conclusion, as pointed out in previous posts, the scenario might require more DM preparation than most do. That is very possible. Sorry about that.
I hope this helps. =)