Yep, the flame will come out. Usually if you wet the wood with a bit of water you can see something closer to the "final" flame. Also, the grade to which you've sanded the wood will decide how much of the figure you see.
If you're on a budget, you might consider winding your own pickups. Stewmac sells the stuff.
http://www.stewmac.com/shop/Electronics,_p...ups:_Parts.html
Of course that's a whole can of worms, and there's just as much to consider as there is in designing a guitar.
Looks good, the lightning bolt is cool.