You're on the right track. Your problem is in your reasoning process.
Did you understand and use variables as I outlined to defines which weapon fires?
The reason all your pellets are being destroyed at once is because of the sequencing of your code.
Pellet > On collision with(whatever) > Destroy pellet
Can you PM me with a link to your capx and I'll download it and take a look. I know what the mechanics of your issues is, I'm just not understanding how use the scrolling.
And is it only 2 weapons you need to switch between or do you need more than 2?