Mark,
I just added a reply to an older topic on screw plate use, so it is now back on the "active" end here.
1. The little lines help the user to match up the two hole thread sets.
2. the two hole thread sets are for making two slightly different threads. The slightly larger is for making the tap and the slightly smaller is for making the screw thread. I am sure that you understand that the tap must be just a bit larger than the screw thread so the finished parts will fit together.
3. You do not need to do a "two-step" thread forming, just go ahead and make the screw thread with the smaller hole.
I surmise that the smiths rarely used "store bought" taps from a catalog. Mostly the taps were made to match the individual screw plate. You will find that, just like any small tap we use today, the expected life of a small tap can be rather short. Also, the spade or fish tail drill bits were made by the smith, he just couldn't go out and buy a replacement #27 drill bit! The tapered reamer was used to gradually enlarge the rough drilled hole to the proper size as measured by a gauge. However, if the original drilled hole is of the proper size, it can be tapped without the use of a tapered reamer.
Jim