As far as guitars go:
Play it, and whatever you think sounds and feels best, go with it. Remember to try the guitar through multiple amps, so you get a feel what kind of tone it generates. Play with the settings on the amp and the guitar, see what you can do with it.
As far as pedals go:
I definitely recommend BOSS pedals. It depends on what type of music you want to play, but I recommend the SD-1 and/or the DS-1. The SD gives you less "distortion", but can be more subtle than the DS. A full dicussion of the differences between Distortion, Overdrive, and Fuzz are way out of the range of this thread, but
http://harmony-central.com has some great explanations and tutorials, and is a good place to start.
General guitar advice:
Play every day. Find tablature to songs you like online, and play them. Don't be afraid to not follow the tab exactly if you think it's wrong. This is the internet. After you get comfortable with that, try working a song out by ear. You may also want to learn play transcribed music on the guitar. It's not too difficult if you can already read music. Practicing scales is a good way to get that done.
Good luck!
Jam it back in, in the dark.