Well now don't worry about the weapons so much. Actually from what I can see you have most of them in nice clean banks of weapon type. That is not a bad thing by itself, but the ship is so insubstantial that the weapons stand out more than any features. If you cut the weapons down by even a quarter, and better concealed them overall, I wouldn't question it. Actually the blasters are the most overused and poorly placed so I'd just remove those. You need to fix the ship though first. Take advantage of being able to depth weapons to the section their parented to by pressing w. This works great for banks of missiles and such that you only want the barrels sticking out for. Try shading the ship, and if your gonna have the big weapons or even all those deflectors and such, try creating bases for them.
As for the ship itself, I think you just need to keep building unarmed ships till the section work and combinations start to look good and make sense to you. It mostly takes repetition and you could certainly move up to the newer sprites but it won't help you get a feel for what fits well together any faster. Actually for the way this looks right now, I'd say try checking out Spoot knight's ships. Good luck