The neck on my bass is very bulky.It has enough mass to safely make it a little thinner.It is a maple neck 5 string with a matte finish.If I alter the shape, will that change the tone?
What product is best to use when I refinish the back of the neck.Is that something that i could do using an over the counter product?

It might alter the tone somewhat. I've found that neck mass can effect tone-at least, it did when I swapped out a P neck for a Jazz. I can't say for sure it was just a difference in mass though. I'd be careful to not take too much off the neck because of loss of stifness. It's hard to tell how much is safe.

You can finish the back of the neck, once all the old finish is removed, with something like Minwax antique oil finish-a blend of oils, polyurethand and thinner. Multiple coats will protect the neck from moisture and you can steel wool it to a satin feel that won't drag on your thumb when you play.

I don't know what tools you plan to shave the neck with. You'll have to make sure that you know how to use them skillfully.