Bad experience with NY registration! Help! Long message but please read.

[UKjohnnycobra]

REgistering my Cobra in New York. I checked the DMV website, followed the instructions to the letter. Spoke to some people in Albany who were helpful but vague. Did all the paperwork (not difficult) Replaced all my lights with DOT and SAE approved items, fitted my bumpers etc even though the Albany people said that "no one would be checking for this, just make sure you have all your receipts for the safety inspection". Made my appointment and hauled the Cobra down to the Elsmford inspection station. Most people there were registering salvage vehicles and the "safety inspectors" were cops. Real cops with guns and stuff.

I have a 1968 302 in the car, which I bought as junk from a sunoco station in Connecticut which specialises in Mustang rebuilds and had rebuilt by a reputable outfit in NJ. The transmission is a 1981 T5 from the CT Sunoco which they sourced fo me from a salvage yard. I am an immigrant to this country and didn't know where to get this stuff and they were very helpful. I have all the receipts for the engine, tranny, rebuild and all receipts for the chassis, body everything down to the last nut and bolt.

But they failed to give me a VIN. The reason? I couldn't link the engine and gearbox back to an existing VIN from the donor vehicle, as you would havbe to with a salvage vehicle. They said each engine and major component has a mark on it somewhere (they wouldn't say where) and my items don't have them. The guy, while friendly. had never dealt with a kit build before (he told me so). I have never heard of these secret marks he is referring to, and doubt that they were in use in 1968 when my engine was built. And he won't tell me any more information because it would help criminals if it ever got out (I'm serious!).
According to him I have an engine I can't use, and he won't tell me what to look for to make sure that any replacement is compliant. So I am stuck.
Has anyone had a similar experience or know the names of individuals in NY who can be contacted for a sane opinion?

Thanks

John