Really, if you do spacemissions like these, build up to that difficulty bioware and don't go from difficulty easy / normal in previous missions, to ultra hard at once with this one. It really sucks the fun out of this game, like this. Me doing my best to get best equipment and then suddenly you get crushed like an ant by a overkill difficulty degree. Do you really think that I'm looking for frustration in a game ? Get real !
You just need to do a lot of "switching" with your shields (Going from an offensive stance to a defensive stance) and you need to save your EMP for when you know you are going to get targeted by the capital ship. It is a bit gimmicky. The upside is once you complete it the first time you'll be able to complete it every time with ease.