The rules state " During the Activation phase, each ship may perform one action immediately after moving. "

Does an Action on a Upgrade Card count as the one action a ship can make after it has moved; or, can a ship use an Action from its Actions Bar, along with a upgrade card's action?

For example, I am flying Wedge Antilles with the Marksmanship and R2-F2 upgrade cards. Can I use Wedge's Focus, plus Marksmanship, and increase his agility (R2-F2's Action) all at the same time in the same turn, or do I have to choose only one of these Actions?

Thanks in advance!

You have to choose one action to take, whether it's from your ship's action bar or from equipped upgrades. In other words, the "Action:" header on some upgrades is a cost - you're spending an action to activate that card's effect. So in your example, after Wedge performs his maneuver, he can activate Marksmanship, or activate R2-F2, or perform an action in his bar.

This also shouldn't be confused with "free" actions. Some cards or abilities will allow a pilot to perform a "free" action which is an action that normally happens outside the Perform Action step (which is the action during Activation you asked about), or in addition to an action taken, such as performing a free action using Push the Limit.

The normal action restrictions still apply. You cannot perform actions while you have a stress token, and you cannot perform the same action more than once in a round.