I'm still hoping someone has a sourced answer, but I came up with a possible answer last night - reverse order.
I was learning Shabbos 104a, where the Gemara gives a really nice explaination of the meaning behind the order/shape of the letters in the alef-bet, and how it reflects the actions and reward of a Tzadik. Since the luchot could be read from both the front and back, after reaching ת, the Gemara gives the meaning of the Atbash of the alef-bet, and how it's an exegesis for Rashas.
Since the planks have rings only on one side, using reverse-order, there can be both a right and left set of Planks. Each set would be distinguishable by whether the alef-bet is going forward or backwards as you look at it from the ring-side. This would still leave me 3 spaces short though (47 spaces, 44 letters).
The solution I came up with is to not label the two corner planks, since they were unique and their placement was obvious (like the corner pieces of a puzzle). And have one Tav shared between both sets.
or msh210's comment: