I would move this thread to the Kingmaker forum for the best help.
Also I would place detailed questions such as yours in a Spoilers heading so as to not ruin part of the AP for those who haven't played/DM'ed it.
This post should be moved to the kingmaker forums. You are likely to get more response there with less risk of spoilers to those playing in the adventure.
** SPOILERS ** Bard, sorry for the length as this is more than you asked for, but includes my own observations from running this AP (we are just starting VV). Kingmaker tends to be a bit swingy in terms of encounters. Some are VERY tough and others your players will blow through. The difficulty also depends on party make up….a sleepy witch, archer, and cavalier will all do very well in this Adventure Path (AP). So the biggest question is what level is the party currently. I would imagine that they are at least 2-3rd it hard to tell by your description since they made a beeline for the Stag Lord. My players found the encounter with the Stag Lord pretty tough at 3rd. Your mileage will of course vary.
So lets talk about the AP in general. This AP is fairly unique in that it is very non-linear. It is a Giant Sandbox for you and your players to play in. If they took out the Stag Lord early you need to draw them into the other encounters…..instead of Starting RRR (especially if they are sub 4th level) maybe “revise” the charter that they would normally get at the end of the adventure…reinforce Brevoy’s desire to have the region mapped before they let the players settle and form a kingdom (maybe pull back the curtain a bit let the players know that each hex they explore is worth XP). The big encounters that they missed are:
1. The Thorn River Camp…..maybe beef up Kressle and she hears that the Stag Lord is dead and decides she should take over as the lead bandit in the area
2. The Kobod caves and the mite caves (works better if they encounter mites first…but really does not matter)
3. The should meet Bokken, Also play up Erastil worship in the area and introduce Jhod, also Kesten Garess should have showed up with troops.
4. Now there are a few other encounters they should hit…and this is a weak point in the pacing of the AP in general….AS OFTEN AS YOU CAN, you need to play up fey activity in the area. Make sure they encounter Tig-Titter-Tut and Pervalish, and also happen across the dead unicorn. Read ahead in the AP to get the feel for the BBEG ,but make sure you don’t show your hand too soon. The PCs should have an eye for fey activity in the area without knowing anything about “her” for a while. But when you reveal the BBEG you don’t want it to come out of left field.
Now when you are ready to have them building their city things to look out for in Book 2.
1. This book (RRR) is even more sandboxy than the first chapter. Things to play up keep the story moving is Troll activity to the south. Also the town stories are important to develop (werewolf, Grigori, and the Gyrona Cult). In my game my PCs heard about Grigori several games before he was a problem…they had actually named the Pub after him…they were caught off guard when he started to try and turn the people against the PCs.
2. PROBLEM SPOTS: The big encounters to watch out for….
a. The Forgotten Keep! This should be a HARD encounter…read up on the Dancing Lady. If you don’t want to TPK your party I recommend having her stop dancing when she initiates a grapple (I had her still be able to dance when she used her other abilities), at least this will give fresh saves when she dances again (and remember if someone makes a save they are immune for 24 hours)….imo this turns the fight into a challenge rather than a likely TPK.
b. The Lizard King….Play up the worship of the Wisps on Candlemere Island. Also try and have the party encounter a wisp before they get here…as when they hit that last hut and encounter super wisp….they should be scared. It is easy to miss but note that the wisp is advanced (and would have an AC of 30!).
c. I don’t have much to say about the trolls or Owlbear as my party was 6-7th level and used good tactics on them. The toughest fight was actually against the Ettercaps and spiders (the PCs got bottlenecked in terrain) but honestly I don’t see them being a problem for most groups…I think it was bad luck.
d. Moving into Book 3 you might need to do some work introducing Varn and his company (Caspar, Willas, and Cephal…etc..) I played Varn as a self-obsessed egotistical boob. He did name his town and company after himself. Come up with your own reason why his kingdom is so small and sucky compared to the PC’s kingdom…play up that problems with the centaurs have severely hampered growth.
More than any other AP Kingmaker is what you make it…and you could even say that the AP is designed for you to do your own thing. Given that, the PCs are almost supposed to de-rail the path….my players checked out the roc nest at level 5 (from VV)…I scared the crap out of them but they ran away and decided that the cavalier really needs a baby roc mount someday. PCs in Kingmaker can get in WAY over their head. I say let them. If they are clearly underpowered go for shock and awe (but from my experience be careful, as some groups simply will never run away). If they can handle the challenge let them try…this is a dice game after all. If you are “linear” minded script out how the encounters will lay out (you don’t have to use hexploration, or even the kindom rules if you don’t want)...It sounds like your players are linear also, you gave them a lead and they went for it right away. So if your players are not the wandering sort, come up with a plan for leads through the story…fluff it out with your own stuff.
Our group has really enjoyed the AP, but I will confirm it is a very different sort of adventure. Again make sure the PC’s know they are supposed to Map the area…that might inspire them to wander around. Good luck.
If your skills are really linear, then maybe this sandbox isn't for you? The campaign is low level at this point and no big plot has been revealed, why not jump ship to something else more to your taste?
* Restov decides that having an uber-magic item is more important than a new kingdom. Switch over to Shattered Star.
* The PCs go to a port city to talk treaty and end up captured by pirates. Swtich to Skull & Shackles.
* You know how I told you this was in the River Kingdoms? Actually, it's an island and you just got hit by a meteor. Switch over to Second Darkness.
As has been noted, things don't really get easier. RRR is a bigger sandbox than the first adventure. VV is a bit sandboxy as well. The later adventures are a bit tighter, but still open.