Dan, yours is a situation we discussed during our deliberations on the steam rule. Bottom line - it can't be addressed in a rule without also trying to address the myriad other special cases that are possible. The waiver process is for that purpose and if an owner/operator can prove the safe condition of the boiler without following the procedures outlined in the rule, it is possible to get an exception.
A message in this thread talked about you being the exception in that you are a fuss-budget with your engine. Unfortunately you probably are the exception since it seems many locomotives suffer more damage while not being used than when they are in service. Because of this it almost leads to a "guilty until proven innocent" situation.
From all accounts I have, Eureka is a gem in excellent condition - albeit the lap seam makes me a bit nervous, only because there are no foolproof inspection methods for that type of construction and historically, lap seams have proven themselves to be less reliable than butt seams.
Despite the fact that steam locomotives may be little used, they are used around alot of people. A catastrophic failure could conceivably jeapardize the entire industry. That thought was paramount in the minds of everyone working on the rule. Airplanes, old and new crash all the time with, usually minimal collateral damage. The traction engine failure in Ohio came within a cat's whisker of being in the news for a long time.
I sincerely hope that the waiver process works as it is supposed to which is that all real concerns are addressed logically, methodically, and with common sense. With verification of proper documentation of maintenance, inspection, layup, and operation that shows the locomotive boiler to be sound, there is no reason that I know of that a waiver cannot be granted.
The FRA is in a tough position in that they cannot afford to set a precedent that less responsible people than you could take advantage of to the detriment of our entire industry. The t's must be crossed and the i's must be dotted.
Good luck.