I agree with Edwin's idea of a homemade jig, especially if your spacing doesn't vary.

That said, this task just screams "Domino". Drilling lots of holes is rough on the wrists, as Mreza said, and I think this is a HUGE consideration. The Domino solves this problem, is adjustable, repeatable, and faster than dowels.

Another consideration is that the Domino has excellent dust collection. Doweling jigs do not. I have a DowelMax and use pocket screws. Both leave lots of annoying wood crumbs all over that constantly have to be cleaned up.

Maybe someone in your area has a Domino you could try out? I know my local Woodcraft always has one out for people to try.