Norm:
I often make commanders for customers. And I make spare heads for them also.
I've noticed that the holes bored through the spare heads have closed up or distorted and are not round any more, after these heads have been on hand for sometime.
Now I don't bore the holes, in the spare heads, until just before a raising, so that I'll have a spare head on hand if needed during a raising.
This is the only experience I have had in storing timbers with pre-drilled holes. Most of the time the frames go right up and the pegs are in, so that if the holes do distort then I haven't 'seen' it.
I'd be care about pre-drilling holes for pegs. Maybe others will have more info for you.
Good luck with your project.
Jim


Whatever you do, have fun doing it!