This is for body woods and characteristics.
http://www.warmoth.com/guitar/options/options_bodywoods.cfm
Here is another for neck woods and characteristics.
http://www.warmoth.com/guitar/necks/necks.cfm?fuseaction=guitar_neckwoods
Choose a combination which sounds like you would enjoy(I would bet money that your strat is alder or maple).
finishes are needed if you want your guitar to remain playable(and not have the neck warp).Other than that,i'm not sure how different finishes(laquers,nitro,varnishes,clear coats,primers)affect the tone...something carvin would know more about than me.
What model are you looking at to customize?
Try once,fail twice...