Ford changed from a 5-bolt pattern where the bellhousing attaches to the engine to a 6 bolt pattern sometime around late 1964 or early 1965, IIRC. That could make a difference. However, depending on what size the "Cobra" engine is (meaning the 289CID/5.0 302CID or the 5.7/351CID), there may or may not be issues...although, IIRC (and I hope if I'm wrong someone will correct me) all Ford Small Blocks (the later 6-bolt 289, the 302, the 351W and the 351C) use the same bellhousing pattern. Can you find out when the engine was produced? You don't need to know the bellhousing pattern, just how many bolts hold the bellhousing to the back of the engine).
If it is a "5-bolt" block...all bets are off. I have no idea if there is any adapter plate for attaching an Audi 016 to a 5-bolt engine.
Hope this has been of some help. There was another "351" engine, referred to as the 351M and later enlarged to 400 CID, and referred to as the 400M, that shared a bolt pattern with the 385 series engines (the 429/460 family). I don't recall there ever being any form of "Cobra" engine that was based on the 385 engine family...but if somebody put one into a Cobra replica and is calling it a "Cobra engine", it might be one of those 385 series engines. They were at one time viewed as only good for boat anchors, but the recent Engine Master competitions have shown them to be quite capable of high horsepower and torque numbers, so someone might have decided to put one into a Cobra replica.
I have a Cobra replica...and my valve covers say "Cobra"...I think it is a box-stock engine out of a 1989 Ford Mustang GT, a very capable engine on its own in a lightweight Cobra replica, but definitely NOT an engine out of an original Cobra...it just has some valve covers on it that say "Cobra". Don't let the name fool you, do some more research and/or insist on some more information before you put any money on the table. If it is a motor from an original Cobra, it could be a great find, those 271HP 289 HiPo engines had a different crankshaft than the 195(?)HP 289 2-V and the 225HP 289 4-V engines...but it could be just an aftermarket SBF engine with Cobra valve-covers/intake on it, too.
Good luck...please let us know what more you find out about the engine, it could be a good find! I dream of being offered an aluminum small block ford engine...think that the weight savings would be worth their weight in gold when talking about the mid-engined GT40 design!
Cheers!
Doug