I was planning to experiment with some new cards and was wonderning about electronic baffle and when ships receive stress. I'm not playing often so wanted to verify the following.

The rules mention 'when a ship executes a red maneuver, place a stress token'. If I use the baffle to discard the stress token at that point am I still allowed to take my actions like focus etc.?

Yup. If you execute a red manoeuvre and baffle your stress away, you will be unstressed when you get to your Perform Action step, and can still perform your action.