I'm not sure if this in the right place, but im pretty sure it's more to do with tone than teqnique or anything else anyway.

Well, what I am asking about is the sound of the pick hitting the strings getting through into my tone, which is obviously quite annoying, doesen't sound too great like that. I don't really have a clue on how to stop this from happening, is it something to do with the gain?

All help appriciated.
Is it a scratching noise? If so, it is most likely how you hold your pick. Do not hit it with the side of your pick if you don't want that noise.

It's the way you hold your pick.

Personally, I naturally hold my pick the same way. Paul Gilbert does too. The scratching sound is good for clean tones, and distortion as long as you aren't able to hear your pick over your amp. Plus, it's easier to pick faster with your pick at a slight angle.
Quote by satchgear
I tried it out in store.

Great neck, nice n light, good tuning stability. Overall a good guitar. I didn't but it cause I generally only buy guitars over a grand now.
Quote by Sean Duffy
No no no, it's not scratching, and i'm pretty sure it isn't the way I hold my pick, it's fine on other guitars. I don't know, it's hard to explain really, it's sort of clicking I suppose.

I know what you mean, happens to me too. Usually, when you first notice it, it's all you notice. But if I forget about it, i don't pay attention to it, and it sounds fine.
The real question is...

do you think an audience will actually care? nope.
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Ah okay. And know I don't need better pickups, my tone is fine from my Seymour Duncans. It tends to happen on certain settings, but I suppose it is true that i'm probably paying too much attention to this, it would probably not affect the sound or make it any worse, especially with drums and stuff.