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Noobish pickup question

I'm making a whamola, and for the pickups I'm going to use the stock ones that came with my bass (I just ordered new ones). So, I took out the pickups and they each have a big rectangular magnet glued on the back. With the magnet, I'd have to make my bridge and fretboard a lot higher, along with adding a nut. Does anyone know if there's any point to these magnets?
It's a J. Reynolds bass, if anyone's heard of it. The electronics are terrible in it, the ground wire somehow came soldered when I removed the pickguard.
 
I'm having a hard time following your modifications, what exactly did you want to do to your bass?

and if I'm following correctly, I don't think wood would help, but I would like to know more about what you are doing.

It's not my bass, I'm making a whamola, which is basically just a pole with one strings connected to a lever at the top to change the pitch.
Crap, I knew there had to be some reason for aluminum instead of steel, besides steel being ten times harder to work with. My dad suggested ceramics, but if nothing else works, I'll just cut out that section and replace it with wood or something. If anyone cares..