427SSSS, no criticism intended
So, to summarize where you are in the process, the NY title takes the place of the MCO in the example in the above referenced thread. Then as has been said above, your insurance card needs to specify a 1965 Ford Cobra Replica, or similar words.
You probably want to get a temporary tag ($25) if the NY registration is expired before driving it to the DPS.
Take that insurance card to the DPS Waiver Site (appointment required) and get it inspected and they will fail it for emissions and then issue you a waiver, good for one year, because they regard it as a 1965 replica.
Take your inspection documents to the tag/title office, with the NY title, the three forms cited in the old thread (includes a tracing of the VIN), and your bill of sale, and I am thinking you will come out with a 2000 ASVE title. You will probably have to make a point that it is an "assembled vehicle." 1965 Ford Replica will be in the comment block on the title. You will probably have to pay the sales tax ...
Good luck!
Sam