At Heartwood school yesterday, I asked a timber framing instructor which order he does his mortise peg holes.
His comment that if you bore the peg hole first and then the mortise you don't have to clean out the "blow out" that happens in the mortise when the peg hole bit breaks the first surface of the inside of the mortise.
Doesn't seem like a big deal until you consider if you have hundreds of mortises in a frame and you have to spend time cleaning out the chips that blow out in each one of them. It could add up to a considerable amount of "clean up" time.
Jim Rogers

Whatever you do, have fun doing it!