I was thinking a Les Paul Studio or some kind of Japanese Paul for like a grand, then a Jet City JCA100 and a 2x12.. And then a pedal? Could I do that? Heres what I want:

I need two channels on the amp. The dirty channel needs to be able to do music such as Gn'R, Led Zeppelin, Mastodon, The Strokes, The Dead Weather, and Foxy Shazam. I want a higher gain distortion (mastodon, guns), and then lower.. for the lower I was thinking a pedal, that I'd use with the clean channel. The thing is, I need to be able to play advancedish chords with the lower gain distortion, and here them really clearly... thats whats important, is that I can hear my chords pronounced, and still have a little dirt.
Oh, and it has to be a Les Paul style guitar. And I need to be able to gig, and have cleans live too (so at least 50 or 100 watts. tube.)

What to get? This is possible for two grand? Thanks people.
For 2 grand you can do SOO much better than Jet City. There is nothing wrong with JC but when you have that kind of money you have MANY options. I would look into a Marshall head of some kind which really will be great for your lower distortion, and you can get those clear, yet gritty chords by backing off on the volume knob on your Gibby LP Studio. Then you can get your pedal to push your gain over the top and get that heavy sound you are looking for. So a JCM2000 maybe...800 or 900 maybe? Thats your call and others will help, too. Then pair that with a 4x12 and you could be pretty happy...

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^ The Jet City JCA100 is better than the JCM 2000, IMO.

Also, OP, the clean channel can do that stuff on its own; it actually has a fair bit of distortion to it, but an OD pedal will still be beneficial. I'd also look into a delay, reverb, maybe a wah for effects.

An Edwards Les Paul sounds right up your alley as well. I'd also consider Orville, a MIJ Epiphone, or an Epiphone Elitist.
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Personally I think the JCA100 is exactly the right sorta thing - if you can wait a while, try the JCA50 when it comes out as well, because personally I prefer 50w amps.

Les Paul wise, I agree an edwards sounds like a good option, but remember to look around craigslist and ebay for used standards and traditionals - but if you're buying used, you have to try it first, LPs can be awful nowadays or brilliant.