Set a variable to Actor Level, Well, you're main character at least. If you're doing level checks, I take it you only have one main character? If you don't this is going to be more trouble than it's worth.
You can set each weapon shop to sell certain items with a conditional branch at that Actor Level Variable.
Actor Level Variable 001 = Actor 01 Level
Conditional Branch when Actor Level Variable 001 == 1
Sell: Wooden Sword
end
Conditional Branch when Actor Level Variable 001 == 2
Sell: Wooden Sword
Iron Sword
end