5' step does not interact with reloading or firing.
As long as you have:
a) reloading down to a free action, and
b)you have two shots loaded and the base attack to fire them, and
c) you have a hand free to reload
then why wouldn't you be able too?
During a turn would I be able to 5 foot step reload/attack and attack/reload if i had rapid reload and pistol or would a 5 foot step take my movement action?
No, it would not take your move action.
You cannot combine 5' step with a move action used to move. You can combine it with a move action used to do something else such as getting something from your backpack or standing up from prone.
5-foot aside, just remember that making two attacks in one round mean using full attack action so if you reload as a move action you can't attack twice.