I am planing to build a custom flying v guitar, i will purchase everything but i will carve my own body, is it worth the extra cost of mahogany if i am just going to paint over it anyway?
You probably don't want maple for the body.
Mahogany is chosen because of the tone, not the look. If you want something cheaper choose alder or ash.

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Its not the look per say, but the tone. Mahogany will sound different than Maple. I like the sound of mahogany a lot, but it's your choice.
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Yes, mahogany sounds excellent
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ok, well the plan was to add a bolt on neck, purely because it's easier, but id prefer neck-thru how do i go about doing that?
If it was me, I'd use both...mahogany with a tiger maple top. Book match the tiger maple so the tiger stripes are angled to accentuate the "V" shape. I wouldn't paint it...I'd either leave it natural with a nitrocellulose lacquer clear or stain the top some color then the nitro clear. Just another option you might want to concider.
I ever u find a Black Mahogany....
it was so beautiful with its brown stripes.

U dont even need to put a clear lacquer on it..
Just buff it to shine...
trust me..
....so little time.