Tinker: You asked about Alchem prods with the rubber coating and projectile length.
The prod will work fine with the rubber left in place... though the rubber may have to be cut away on the edges if you're mounting the prod with Alchem's small bow-irons. The rubber between the prod and stock will slightly reduce noise and apparent recoil, but it certainly isn't necessary for satisfactory shooting.
For projectiles, you might as well start with 11/32nd inch standard arrow-shaft with 125 grain heads. (100 grain may give you slightly better velocity at shorter ranges, but will wear strings out faster) Medieval bolts generally run anywhere from 12 to 18 inches long, with an average of about 15 inches. My SCA customers, who shoot in target competitions at 20 to 40 yards generally prefer longer bolts rather than shorter. 16 inches is the most you can get from arrow-shafts if you cut two each. I make a lot like that. Theoretically longer still should be more stable, but they will have more surface friction as well as weight, so they'll lose velocity faster at longer ranges.
You definitely want your bolts to have a forward weight bias (which is a fair argument against using butt-caps). The experts say the balance point on your bolts should be about 1/3 of the way from the front.
As for thickness, many of the bolts you see in museums are very thick, 1/2 to 3/4 inch seems about average, and the preferred woods for medieval bolts were ash, birch or oak, but for the sort of lightweight bows we shoot, you'll want to stick with standard arrow-shaft to begin with. Spine weight doesn't particularly matter, so long as all the bolts are spined the same. Of course it's possible to get a shaft that's simply too wimpy, but if you get shafts spined for 40 to 50 lb or thereabouts, you'll be fine.
Remember that crossbow bolts must be very straight, have the heads on straight, and if you're using un-nocked bolts, make sure the butts are square as well. If have seen un-nocked bolts cut with a slight hollow in the butt. That seems to work out well, and it may be a cure for a marginal misfire problem.
I'll think about it, maybe come up with more ideas, but that oughta be enough to start with. Geezer