I just read through this build and...man, that is one awesome car!
I think the whole "numbers matching" thing is a tricky topic. 1966 saw 66,843 SS 396 Chevelle's produced. If this car was optioned the same as 40,000 other cars (besides paint and interior, what else was there?), I don't see why it's such a big deal. In fact, only the 2-door Malibu had more cars (130,540) built that year than there were Super Sports so, rare it was not. So, unless he managed to find some rare 1-out-of-10 combo and tore that apart, let it be.
This car is awesome, he put some incredibly thoughtful work into it, and it's now a really cool driver.