As I understand it, and I've studied it for some time, matching numbers started mid '66, like Beaverbikes sez. The '67 -Y (dash Y) indicated a mid year wiring change, where the zener diode was moved from under the seat on a plate heat sink to a finned heat sink under the lower triple tree, requiring a different wiring harness. This -Y appears only on the motor.
The bikes with the Y and no dash are 1970 bikes with what appears to be '67 numbers (but all the later model's features, like unc threads and fairing lugs on the steering tube.) The Y appears on both the engine and frame on these bikes. There are stories about leftover bikes and dock strikes most of which have been debunked. My personal theory is that it was a scheme by then financially strapped BSA to convince the British government that these bikes had already been taxed. (British taxes were high enough in the late '60's that most of the Beatles and the Rolling Stones moved to the United States.)
The way the bikes were numbered changed again in mid '69. An early '69 Lightning, for instance will start with A65LC (the C being for the '69 model year.) Mid year the numbers started with two alpha characters for example DCxxxxxA65L, the D being for March and the C still being the '69 model year. I have a '69 Lightning (CCxxxxxA65L) and a '70 Lightning (A65LAxxxxY) one of the Y bikes.
And Tony, you're right about the '65 and earlier twins all having A50 frame designations, and the 650's having A65 engine designations, but according to Bacon and the 30 or so threads on the subject at Britbike.com, the numerical characters themselves did not match either. In fact I'd be pretty suspicious of a bike that did.