Werowance.--P.D. is the pitch diameter, not the root diameter of the gear teeth. O.D. is the outside diameter, but you don't have anything on that chart that tells you what the root diameter is. When you mesh two gears, the center to center distance is 1/2 of the pitch diameter of one gear plus 1/2 the pitch diameter of the other gear. If you are making your own gears, I don't think you have all the correct information for doing it. The center to center distance in the downloaded plans is correct for the center to center of the correct gears as purchased from Berg. What you should do now, if you have kind of lost your place, is to take the two gears you have, mesh them with one and other, measure (as best you can) the center to center, then use that measurement to drill and ream correct size holes for stub shafts in a scrap piece of material and put the gears on the stub shafts and see if you can easily turn them by hand to see how they mesh. Once you have determined what that center to center distance is, you can use that on your engine. To plug a hole in aluminum, I generally turn a plug about .0005" larger than the hole to be plugged, cover it with Loctite, and press it into place. A vice can work to do that. Let it set up 24 hours, then file it flush on both sides and put the new hole in the correct place. The old timers would put a cigarette paper (which is 0.001" thick) between the two gears when they meshed them to give a little "running clearance". I don't do that myself.