My guess is that you have the distortion up full, try bringing it down to about 60-70% - it will actually make everything you play a lot clearer. Also, try switching most of the tone settings to around 60 percent (adjust to taste). The noise you mention could be a combination of the pickups you are using, damaged or low quality leads/cables and sitting too close to the amp/pc monitor or other electrical equipment. If you are looking to upgrade your pickups, try Dimarzio Evolutions - they are great all rounders, very hot with high output, great for rhythm and lead and for controlled feedback. Beware though, they will force you to play better because you will hear your mistakes a lot more clearly! Not a bad thing for improving though;-)
I'd lose the noise gate all together or else turn it way down, if you have it turned up very high it's because there is a problem with your set up or you are sitting too close to something that is causing electrical interference. Hope that helps!