In reply to Tony Naylor:
I think if the fixing are matches (i.e. is the same size) then the only difference with the neck would be the orientation of the headstock; I think the bolt arrangement would be symmetrical. It might be though that you do need to be careful to buy the correct sized neck to fit the body, which would be the main difference between a left- and right-handed guitar.
In short, I don't really know. Have fun!
(These look like they expect the neck pocket to be a standard size.
http://www.warmoth.com/Guitar/Necks/Strat_WarmothPro.aspx)