The vin number will begin with the digits "242" on a real 69 GTO. On the original engine, you'll be able to find the serial number portion of the vin (last several digits) on the front of the engine block, down low, next to the passenger side of the timing cover. (Don't confuse this with the 2 character id code and the numeric sequence number that's also on the passenger side but up high, near the cylinder deck.) If this number doesn't match the vin, it's not the original engine.
The vin should also be on top of the frame on the drivers side, between the rear wheel and the end of the frame. This one is very tough to see with the body on the car unless you get lucky with a mirror.