Hey guys, just thought I would get back to you all and let you know how it went.
I firstly want to thank you guys, for making it clear to me they will do things much differently than what I think they will. That happened A LOT of times during our session, and it was so nice to have the tips in advance.
I did insert an NPC that my players really did take a liking too, and I put him under the mentor ship of a head priest that one person in the group found was evil. I am thinking of making it a little side quest to do for when I want to drop the campaign for a bit, or just use it if I am not prepared enough for a session. I was thinking of having the head priest kill the NPC (who happens to be a priest as well under the head priest) that my players have grown to like, but I am not sure if that would be a good idea or not.
For the evil priest, I have decided (since SPOILERS! Cthulu does appear in the Carrion Crown AP we are doing END SPOILERS!) to make him a follower of Cthulu, as my group are all lovers of the game Arkham Horror, and therefore are familiar with all the old HP Lovecraft references.
I did mess up on combat, quite a few times actually, but I hope I will do better during the next session and luckily nothing major really got messed up during our session.
I did do a few random encounter to screw with my characters, they worked well but I would rather not do them too much, as they did kind of mess with the flow of the whole thing.
For scaling the enemies, I added about 20 hit points, doubled amount of creatures, and still managed to not make any combat seem too daunting. I think for my next set of encounters I will add a good plus five to damage rolls, plus three to damage, plus 4 to AC and a good ten or 15 points extra to each and every creature they fight. If nothing else, things should get interesting. To keep this from killing them (as it could be way too overpowered) I am going to give them a couple of cure light wounds potions (given to them from the NPC they like) to make sure nothing too drastic happens to any of them.
Any more advice, suggestions, or ideas?
Once again, thanks to all for your help.