How the hell does jonny get that bassy tlove it but I do feel it's to trebly. Do I need to change my pickups to humbuckers or maybe I need a good clean amp like a fender twin reverb or vox I'm currently using a marshall AVT solid state amp anybody have any ideas?
For one, I'm just going out on a limb here, try the neck pickup. It's alot less trebley than the bridge pickup.

He uses a Fender Telecaster Plus. Which means a has a Lace Sensor Blue pickup in the neck position, and Lace Sensor Red Duallies in the bridge. Duallies means that it's two pickups wound together and they act like a humbucker.
Along side that, they have a talented guitar tech, who has probably modified the guitar further. Well he's added a kill switch anyway.

Pedals wise. Well he uses a Marshall Shredmaster, a discountinued 80's pedal which is pretty harsh, but interestingly he uses it in conjunction with a Boss SD-1, not sure how it works to be honest, but I think he has the SD-1 going to a Vox AC30. These Vox's are special in that they we're produced in the 1990's so the circuits are different or something. He also has a Fender Solidstate amp. I forget the moment. I think it's an 85, but I might be wrong. He basically has the shredmaster alone going into that.

Other pedals. Akai Headrush MK1, a EHX Polychorus. There's a few others. I'd recommend popping over to the Harmony Central forums, go into Effects, and there's a big thread called Post Pictures of Jonny Greenwoods pedal board.

With regards to your amp, I think it could cater for the Distorted tones possibly.

Ultimately. My advise is. Yes, try to replicate his equipment but to a point. At the end of the day your playing the guitar, it's your mindset, your touch, your feel and most importantly, your imagination being inflicted on the guitar. If Jonny's tone gets you further to what you think YOUR ideal tone is, then good luck.
neck pickup, tone down a bit, and turn the treble and gain down on the amp. i can get a pretty decent tone with my hot rod deluxe and my strat.

jon greenwood is amazing.