Fippy,
I think you may be getting a little mixed up by the photos of Chuck's excellent model. It's surprising how much such things as the relative heights and rakes of masts can be distorted due to such things as camera angles and the changing focal length of a zoom lens.
My suggestion is: trust your plans. They've been worked over by several generations of good designers. That rigging plan is, in fact, a full-size drawing of all the spars in the ship. Take your measurements from the drawing.
The dowels that come in the kit are just raw materials for making the masts. They have to be cut to length. You need to figure out how deep the hole you drilled in the hull for the mast is. (Just how deep doesn't matter, as long as (a) it's deep enough to make the mast sturdy, and (b) you know how deep it is.) Measure from the plan the length of the lower mast, from the deck to the lower masthead. Add the depth of the hole in the hull to that figure, and you have the length to which the dowel needs to be cut.
I imagine the masts also need to have their taper added. You can take the measurements for that from the rigging plan too. (Don't try to convince yourself that the masts don't need to be tapered. If they aren't, they won't look right.) As I imagine the instruction book explains, the easiest way to taper a spar is with an electric drill. It's easiest to do before you cut the dowel to length. Clamp your drill in a vise (or Workmate, or some other means of holding it steady). Chuck the lower end of the dowel that's going to be the mast into the drill. To keep the dowel from flying around and breaking, hold the other end in your left hand (assuming you're right handed), with a thick, soft rag to keep yourself from getting burned. Then turn on the drill go to work with a sheet of medium-grade sandpaper. Fold the sandpaper into a pad, and keep it moving up and down the length of the dowel. It may take a little practice (and maybe a trip to the hardware store to buy a replacement dowel or two), but you'll quickly pick up the trick and you'll find that tapering a mast is quite simple - and quick.
If I remember correctly (as I may well not be doing), the yards, gaffs, and boom have some taper already turned in them - though they may need to be touched up a little. Again, you can take the dimensions of them from the rigging plan. Maybe it's worth noting that the draftsmen who draw such plans almost always employ a convention that's slightly at odds with reality. The draftsman draws the yards as though they were swung around parallel to the ship's centerline. In the real ship that couldn't be done; the standing rigging would get in the way. But drawing them that way makes it easy to take their dimensions from the rigging plan.
Hope that helps a little. Good luck.
Youth, talent, hard work, and enthusiasm are no match for old age and treachery.