what kind/size of bedrooms do you use? From what I can tell, the malus from being in a communal room remains for some time while one from having a cramped room is gone as soon as they leave the room and I read that their morale is unaffected while they sleep.
I just do small 2x2 or 3x3 bedrooms. The mood penalty from a small room isn't that bad, and will go away over time if they spend most of their time in nice open areas. The other room attributes don't matter much unless they spend a lot of time in their rooms, which most do not. Also what is a malus? Google tells me it is a type of shrub, or a return of compensation upon deficient performance in a contract.
How do you do the organ transplant stuff? Is there a way to preserve them? I know things don't rot below freezing temperature, but I'm guessing that's not good for organ viability.
I don't think organs decay at all right now, unless it was recently added.
I know the colonists can build up an immunity to the same morale bonus, but can they build an immunity to bad ones? Is there a way to make them care less about certain horrible things, like butchering raiders?(I've got a valuable cannibal I like to keep happy) Alternatively, is there a way to turn everyone into psychopaths or cannibals?
You're mixing two things up here. Colonists who perform the same joy activity over and over to fill their joy need will begin getting less benefit from it, so you need to mix up the number of 'joy activities' available. This doesn't directly impact your colonist's mood, and is different from the mood bonus/penalty effects such as seeing a dead body. They do not 'get used to' doing something like that. A colonist with the cannibal trait won't mind eating human meat, and a psychopath I believe won't mind ANYTHING related to violence, but you can't train the responses out of colonists by repeated exposure.
I've noticed that animals that die outside of the home area end up forbidden, but in the interest of not wasting/losing animals(I'm worried they'll run out) to predators, I'm looking for a way to easily get those corpses. I know i could make the home area cover the whole map, but then the colonists would try to clean the whole place. Failing that, is there a way to easily locate corpses or notice when an animal has been killed? I play on large maps and scrolling everywhere to see if anything has died recently takes a while.
I don't know of an easy way to do this. Some mods might be able to help but I don't know if any cover that particular aspect.
What affects a prisoner's chance to be recruited aside from the social skill of the warden? Does their mood affect the likelihood of them accepting? Should I have them in a fancy room?
The prisoner's mood and the social skill of the warden are the two most important factors as far as I know, but there appears to be another modifier that isn't really shown where people of other tech levels are reluctant to join if yours is different. By this I mean if you have captured a tribal, he will be much less likely to join (more difficult to recruit) than the exact same character from an escape pod. I could be wrong there, just my experience.
Aside from having more bodies to throw at enemies, is there any advantage to having a high population? Seems that once basic jobs are covered anyone else is just a resource drain and takes up space with extra bedrooms.
Yes and no. Keep in mind that this is a game where anyone can be suddenly laid out and unable to work by disease or injury. If you only have one good cook and he gets Malaria, your skill 2 cook might cause everyone else to get food poisoning. If your skilled doctor is himself injured, who patches him up? Its sometimes worthwhile to have redundant skills.
Is animal breeding a decent way to get meat/leather or does it take too long? I know different animals take different amounts of time to mature, what are some animals with a good growth time to resource ratio?
I've had success with chickens as far as meat/eggs, and alpaca are great for getting wool. Some animals have such a long birth/growth cycle that they're not worth it, like elephants.
Even with what seems to be decent(12) shooting skill, my hunters take forever killing stuff because they engage animals at extreme ranges and miss almost all their shots, is there a way to fix this?
There are a few combat realism mods that revamp accuracy and stuff. You can see WHY he is having a bad time if you select the colonist and hover over the target (best done while paused) as it will list all of the bonuses/penalties.