There are a couple of things that is driving me crazy at the moment and I want to solve them so I can record once and for all. It's been two weeks and still I'm not satisfied with my guitar sounds.

First there was too much buzz and I fixed by adjustments. But when I use the bridge pickups there is still vibrating except if I block all the strings untop of the ones I'm playing (which is difficult). So I use the neck pickups and the sound is more clear but it has a fatter sound. Does it buzz when I use the bridge pickups because the pickups are closer to the strings than the neck pickups? Do I solve this by lowering the bridge pickup farther away from the strings. If you have active pickups there is no need to worry about pickup height, action and neck relief?

When I'm playing the fifth and sixth strings (G and D) they have a very low unclear diffused vibrating sound. So basically it sounds like crap when your playing power chords (since you use those strings most of the time for them). I don't know why they sound like that. Is it because I just need to switch the strings? Or can it be that I'm tuning my guitar to D with 9-42 gauge?

try 46-9 strings, or 52-10s.

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I would use 10s for D, and try lowering your bridge pickup a bit.
If it still sounds dodgy, I'd suggest taking it to a shop and getting it looked at.

With active pick-ups it recommends that they be placed as close to the strings as possible. If you are not using actives I'd try backing the pick up away a little from the strings see if that helps, you can always adjust it back if it's not that causing the problem.
As for the unclear tone with power chords.....is it fret rattle do you think? Are the strings catching on a fret higher up which is creating this dull tone?
I'd put heavier strings on for detuning and maybe raise the action a little to see if that cures the problem, if it is rattle.

You don't say what guitar you are having problems with or the set up? But if it's really not working I'd do the above mentioned thing and let a tech look at it.

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I use an Ibanez gax 70 (ax series). The action is 2.0 mm on the bass side and 1.5 on the skinnier strings. The neck is adjusted correctly cuz I can fit a business card in between the 6th fret when I hold the first fret and the 12th fret.

The buzzing you explain. Its from the strings, not the amp, right?
Anyways, I think its just that you tuned to D, and 9-42 are not thick enough, thus causing the strings to flop around too much.

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for D I have to use 12-56 on my ran. If I use 11's its to loose for me to do any good trem picking. I just resoldered my emg's into my explorer the other day and popped some 10's on it and its wayyyy buzzy and tuned to E. I dunno what the fuck is up, but tonight ill try some more adjustments.

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The best guitar tech in the place I'm at was my original guitar professor when I first started out playing guitar. He uses the same pedal as mine, so I went and brought my guitar so he can check it out. Surprisingly my guitar sounded really good when using his amp and pedal with no buzz and dull sounds. So that means their is nothing wrong with my guitar but either with my amp or pedal. So I'm going to bring my pedal and guitar again to his house to compare to see if my pedal is working properly. If it is than my amp is fucked.

hope it all works out.

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The way to problem solve a rig, is to take it to the bare essentials: guitar > lead > amp, then if thats ok, add one piece at a time until you find the problem

lead as in cable?

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Yep. Invest in some really top quality leads/cables as cheap ones crackle and pick up all kinds of inteference.

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After I saw there is nothing wrong with my guitar and pedal by trying it out at the guitar tech's house I came to a conclusion it must be my amp. Than I was thinking maybe it isn't my amp but the signal is being affected by some kind of electrical interference in my house or my amp picks up weird electrical sounds. When I play a note in my house it makes strange whistling alternating, vibrating electric noises. I know this is some kind of electrical interference. My question is what the fucking hell is making it! At the guitar tech's house there are many more cables and amps everywhere but still the sound is perfect whereas at my house there is much less cabling and objects and still there is some kind of weird electrical interference! I don't know if this has to do with it; but could it be because my amp picks up weird electrical sounds because when I speak or scream I can hear it echo through the amps speakers! Is that normal hearing your echo through the amps speakers? I use a Trace Elliot C100 and it looks much better than it sounds. Well getting a new amp solve this problem? I want to be sure because I don't want to waste money buying a new amp and still have the same existing problem.

Yipee I found what the problem is finally! Everything is working properly except I was getting too much feed back which made my dam guitar buzz and make whistling noises. The reason I was getting too much feed back is because I'm using a 100 watt two speaker amp in a small room which was too much power for my small recording room. The reason why I never had this problem before was because I use to work in a bigger room while recording but had to move to the small room I'm working in now. The big room gave me enough space so I won't get feed back. It isn't a problem for me getting a smaller 30-60 watt one speaker amp because I usually record and recording doesn't require that much volume and power because I place the mic right at the speaker. I just care about getting a good sound with no need of excessive power or volume.