Ah, it's not that bad, if you're uncomfortable with playing at a faster speed you should slow the tempo down to something you can handle. And when you've got that down pat, increase it a tad, maybe 5 to 10 bpm, but don't do anything you can't handle. If it hurts, you're doing something wrong. I still get lost with the metronome, so don't feel bad about that, I have a horrible sense of rhythm which I work on (not often enough though). Anyway, I'd suggest starting each practice session at 100 bpm tops then work from there. It'll be boring as hell, but you're practicing, what's so fun about that when you could be playing? Well, it's a necessary evil... if you want to get better anyway. Just take your time and you'll be fine.

Oh and when watching Petrucci, just remember, he graduated Berkley, so he's easily on a much higher level of education and experience.