The modules should be used at the right time during each mission. For example, using the EW pod when entering the minefield (you know which one) and then blowing EMP when close enough to damage the frigate while also taking out the rest of the mines.
You should also be constanstantly toggling the power conversion module. Always in attack mode when firing cannons and in defense mode when not (unless shields are already full).
I find the difficulty just right with Grade 7 gear with some missions such as the escort one being particularly easy. Keep at it, the missions get easier when you get used to when certain 'events' occur.
I find the space missions difficulty just right as well, and have no trouble running through them, occasionally, as in once every couple weeks, I'll die on one, and thats it, they are extremely easy once you know what to do. They are far from too hard, and just take practice.