Lately I have been working alot on alternate picking. Things are going great, however I'm still having a little bit of trouble when descending. Mainly, finger independence and making notes sound flat because I don't lift my fingers up at the right time.

If anyone can recommend some exercises to address this problem specifically, I would appreciate it!
PRS Custom 24
Orange Tiny Terror Amp
Mesa Boogie 2x12 Rectifier cab
Boss EQ
Dunlop Tortex 1.14mm picks
D'addario 10 gauge strings
Usual thing, start slow and practise with a metronome at a speed you're comfortable with, then progressively speed up. If you start to get sloppy, slow down again.
I would advise you download this one (it's free) http://www.nch.com.au/metronome/index.html

That way you can use it when you're not on the internet, unlikely as it may seem :p
Ibanez RG1570 w/ Bareknuckle Pickups
Ibanez RG655
PRS SE Fredrik Åkesson Singlecut
Blackstar HT-5
Harley Benton G212 Vintage
MXR M-108
Digitech Bad Monkey