For what it's worth I generally primed after all drilling, deburring, counter sinking and dimpling. Occasionally I had to run a tapered awl or drill through a stack of holes to get them aligned and the rivet in.
I prepped for DuPont Variprime with their etching system, usually after scuffing with Scotchbrite. I gave up on Alodining before the prime coat early on. Some of the HS parts were Alodined only.
I have also used Marhyde grey rattle can primer on small parts, some times with just a scuff and acetone clean before hand.
A few alclad parts I left bare - empenage skins, shims, tip-up canopy seal angle, etc. I primed the canopy frame after assembly - it is already partially assembled with welds when received.
I used to keep a few ounces of left over Variprime in a jar to touch up any cut edges or holes drilled after priming using a cotton bud. The Variprime seems to last for ever - if you keep it shaken, or poshibly even shtirred Mish Moneypenny.
I guess I was experimenting and learning. Perhaps next time I'll do it differently and more methodically. I like to keep things simple, light and economical so will probably go with only priming non alclad parts.
Jim Sharkey
RV6 Tip-up - getting there!