Feat Stacking

Does the +3 from Skill Focus: Perception stack with the +2 from the Feat, Alertness?

Yes.

http://paizo.com/threads/rzs2opva?Does-Alertness

Does the +3 from Skill Focus: Perception stack with the +2 from the Feat, Alertness?

It most certainly does.

Same ruling for the Prodigy Feat?

I believe that all "untyped" bonuses stack. If it does not list a type, like "morale, "divine", "racial", ect., it is classified as "untyped".

Yar!

I believe that all "untyped" bonuses stack. If it does not list a type, like "morale, "divine", "racial", ect., it is classified as "untyped".

^ This.

Dodge bonuses stack. Racial bonuses stack. Circumstance bonuses from different sources stack. And finally, untyped bonuses stack (that is, the ability does not list a bonus type, such as if it said "you gain a +# bonus to x" or even "You grant +# to x"... neither of those list a bonus type, ergo it is untyped, ergo it stacks).

SOURCE

In the above cases of untyped bonuses, while the bonuses both come from feats, they are different feats - thus different sources - thus they stack.

my beef is that this rule is not easy to find. There are several spots where Bonus and even stacking of bonuses is mentioned, but none of them go into detail as to what actually can and can not be stacked except for that one spot in the magic section. :/

~P