Your iron should be fine--40W is plenty of power. The main difference I find between pedal work and amplifier work is the size of the iron tip I use. I have a fine chisel tip (~1/16") that works great for pedal building but doesn't have enough thermal mass for the larger things you'll be soldering in an amp build. I'd recommend a 1/8 - 3/16" chisel tip for that.
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