When I did mine I did the countersink first. No hole for shavings to get into at this point.
After seeing the jig and how it works, and how tight the tolerances were on those pieces, I didnt think it was a problem doing the countersink first. Normally I would think that doing the countersink first would give alignment problems and make it so the main hole was not drilled straight. That may be a problem when drilling by hand. Or at least make it harder. But with the jig it seems thats not a issue. You should be able to drill the countersink first, then drill the main hole and have it go right in, in the proper place, depth and all that. -- Worked for me.