I have been thinking about your "problem" for the past few days. I have used a two-stone method almost exactly like yours for some time and have not experienced a problem of an overextended bake time. I have an electric oven (which I assume you have) and put the first stone on the lowest oven rack and the second stone on the 4th rack up from the bottom, just under the broiler element (I, however, don't turn the top stone upside down).
I think the problem may have been the starter or its use in such a small quantity (1/2 t.), without any accompanying IDY. If the starter was not mature enough, or even if it was mature enough, its use in such a small quantity in a dough that is subjected to retardation (as the Lehmann NY style dough is), the fermentation may have been inadequate (too little) to release the natural sugars from the flour. In such case, there wouldn't be enough extracted sugar to promote browning of the crust in the normal manner (through caramelization of the sugar), and the natural inclination would be to continue baking until the crust turned brown--which could take much longer than a typical 7-8 minute time period. You didn't indicate, but I would guess that the dough didn't rise much, either while in the refrigerator or during the warmup prior to shaping, as further evidenced by the lack of a pronounced oven spring. On the other hand, if there was a significant rising of the dough in either the refrigerator or during warmup (which is somewhat untypical of the Lehmann dough), then the only explanation I can offer for why the crust didn't brown up in the normal manner is that the dough overfermented and all the natural sugars were exhausted before bake time such that little caramelization could occur. For this to happen, the dough would have had to have been in the refrigerator for quite a long time, maybe several days. In that case, you could also experience little oven spring because the yeast was heading south at the same time as the sugar.
Does any of the above sound familiar?