Any good hardware store can probably sell you a jobber's length #29 drill bit. The problem with that is that they aren't long enough to reach all the way through the rails or allow you to place a thwart knee rivet where it is the most advantageous. These are 6" long and they are also very handy anywhere you need to line up a fairly long hole for a rivet–boring down through an oarlock pad and through a rail, for example. We buy these for use in our own shop, and so have them on hand and are making them available to you.
This is the way it's done. Position a straightedge (in this case a 2' folding rule) with the hole's centerline, and align the shank of the bit parallel to that. It's a simple approach that works extremely well. [This photo is from the Duck Trap Wherry CD.]