Hmm, also an engineer, and also having a big A-10 kit (fiberglass version) there are various ways around this.

First, I don't see why the balsa joint has to be over the wing even using 36" lengths. THe chord of the wing is not over 36" so obviously a single piece could span it.

However, with a 1/4" plywood doubler( I assume it's a one piece doubler) and a good scarf joint there is no real risk whatsoever from putting the splice over the wing. If you want some insurance, put some structural fiberglass (as opposed to lightweight cosmetic stuff) over the joint on the outside. If you like spending money, upgrade to CF.

If you want the best scarf joint, angle it not only from the vertical, but also thru the thickness of the wood. That would require precisely matched cuts in each piece using either a jig or a good bit of sanding to fit.

Lastly, I'd like to hear the $$ amount you plan on spending for balsa & ply here. If it's a whole pile, you'd be better off buying the glass kit from Dean Lassek for around $1500.