Scenario: I have Proton rockets and Counter Measures on Dash Rendar.

I use my counter measures at start of combat, increasing Agility and removing a target lock. On my action, I fire my proton rocket at a ship at range 1. My agility is now 3. Will this give me a 5 dice roll, or am I still relegated to using the agility that I have on the Dash card?

Your agility is 3, so you will roll 3 additional dice.

The god of cheese (all praise unto Him) is correct. Countermeasures specifically states that it increases your agility for the entire round, so anything that would refer to your agility includes this bonus.

Don't worship me, apparently I'm just a troll.