If your haveing a harsh bright problem its prolly the maxed out presence knob.Presence on a Marshall tends to make things bright and brings out the buzzyness of the pream's distortion.
I use a JB humbucker equiped strat into a 50watt Marshall and 100w cab.My settimngs are Presence 4,Bass 6,Middle 4,treble 4 1/4 try this as a starting point with your gains set to your taste.You'll have to tweak as you have a diffenant setup but this is approx were most of my Marshalls end up with a HSS strat.