First I would just like to say that I am a new member and have already learned quite a bit from reading all of the "sticky posts" for the past several hours. So Thank You everyone
First of all welcome to the site I am glad you found us and liked all the sticky's.

I have two questions:
I have two answers.

How often are you supposed to handle baby ball pythons?
I try and handle baby's every couple of days for short periods of time from 5-20 minutes.

Specifically, after you first get it- before and after feeding- for how long each time-
Right after getting them it is usually recommended that you give them about a week of no messing to settle in. Before a feed is fine but after should be avoided for two reasons: one some Balls stay in feed mode and may think your fingers are second helpings and two They feel really vulnerable after feeding and may on rare occasions regurge the meal and this is very stressful on your snake

and what kind of harm we are talking about for over handling. I have read many different opinions on this but this community seems to have experience so I would like a few more! It seems like the more you handle them, the more they will get used to it as long as they are continuing to feed?
Every animal is different some Balls get quite use to being handled while others don't really take to it. You'll need to get to know your snake and see what it likes. Don't rush things you have a long time to get things right, take it slow and learn to read your snake and you will both be far happier.

Does it only work to rub f/t on mice or rats? What about gerbils, hamsters, ferrets, hedgehogs, etc. LOL- I know this may seem rediculous but some of the rodents I have access to and some I do not so in addition to making sure the environment is where it should be, I also want to know if I can assist the feeding process in other ways. Thanks a bunch everyone!
Typically the scent of the F/T feeder is enough to get the animal to eat (if it is already eating F/T). So there is normally no reason to scent a F/T feeder. Remember Ball pythons are imprint feeders meaning they get their mind set on what is food and what isn't. So If you scent a rat with mouse scent and they get fixed to that you could run in to problems later if you can't scent anymore. Your snake may see a rat that doesn't smell like dinner. Keep in mind 95% of a Ball's feeding response is scent related so if it looks like a rat but smells like a mouse when you offer a rat that smells like a rat it might not think its food.

Keep up the research and never be scared to ask questions thats how we all learned