This is my first guitar which has a floyd rose, and i re-strung my Ibanez a few months back with a 42 gauge set which turned out the be the wrong gauge lol =/ so my bridge has sunk into the body a lil bit so I'm hesistant to use the whammy, but thats not really the issue.

I've come to the stage now where I could do with a change of strings and I want to clean my guitar as well. I was wondering if anyone could recommend a set of strings I should use? Soundwise as well, I tend to play hard rock/metal so any suggestions would be awesome =]
It's not that you're using the wrong strings, it's that you haven't adjusted your FR to compensate for the different string tension.

Look up one of the FR set up guides here, I've never had a guitar with a FR so I don't know how to set them up very well.