You pulled your old axles out and didn't notice that it took the dowels with them? Just get new dowels put them back in and bolt your axles back in.
Are you trying to increase strength in the rear hub to axle interface by drilling new hardware holes and going to larger bolts and dowels? If so I would suggest you pull the hub, take it to a machinist and have it done correctly. Yes I know a company that sells new dowels with a drill bit. I would still do it right.