Congratulations on the car! I too have a 66 and did quite a bit of research before and after the purchase. IMHO, I think it depends on your long-term aim for the car- keep it and drive it or flip it. True #s
matching and low miles drives up the price but if you want to keep it and drive it with a retrofitted tripower/4 spd setup you should go for it.
If you check values on places like Hemmings, you might get a better idea of what it could potentially be worth and if that value is worth keeping a configuration you don't necessarily want. As with all of these condition is everything. Factory 4 spd with tri-power are the highest value for the collector market so if that is what you want to do, I think you add value for resale in the future but maybe not for the collector purist looking for all original but even with that, the market has not really caught fire on these cars. No significant spike in prices make it hard to see who values what.
Query Mecum, Barrett-Jackson and other auction sites for a historical search of actual sales to see what is valued.
I have tried to find the production #s
on my car was well and after almost 2 years I still haven't found it. The big #s
are easy (convertible, hard top, post etc.) but anything more than that is challenging. If you do find a location that has that level of detail, I'd like to know!