The rule makers are pretty smart people and I think they have worded this pretty carefully. It's very important not to read your own additions into the printed rules. Here's the relevant paragraph -
12. K.VINTAGE FUEL (VF)
The engines production date shall be prior to 1956. Flathead, OHV,
and two-stroke engines shall retain the O.E.M. heads, cylinders, and
crankcases originally installed at time of factory production. Above
components produced after 1955 and exact reproductions may be
legal in vintage class if they offer no competitive advantage.
Documentation may be required to prove authenticity of vintage
design.
Allowable overbore in this class is +0.050 inches over O.E.M.
standard bore to remain in displacement class. Further increased
displacement beyond the class limit shall place the motorcycle in the
correct class.
NO FUEL RESTRICTIONS. See Chapter 2, paragraph 2.F.
What it says specifically is you must retain an OEM or exact reproduction head on the cylinder. Note that it does not say you can't improve its performance. One of the tricks to going fast is not to read things into the rules that aren't there. If you have a specific question like the dual plug question you can get the definitive answer at tech@bonnevillespeedtrials.com. Be patient, this far ahead of the event the people who put it on often have a lot of other things going on in their lives and it can take a little time to receive an answer.