I have not seen a taller valve cover on a 66 stock 289 in the last 20 years I've been working on these cars everyday, but I learn something new everyday. Maybe I'll see some soon, but I won't hold my breath.
The change was not to the height from top to bottom as much as to the angle of the top. Mid year they became squarer, so that the area around the breather was flush to the top rather having a bubbled area. The other change was the notches they put along the gasket edge to accomodate the Thermactor (T/E) sytem air logs for the California "smog" equipped cars.
My July built 66 GT fastback I had years ago had the later style 67 valve covers, as does the Aug 3, 1966 coupe I am parting out right now, both had the original drivetrains and were Dearborn built with vins over 700,000. My April 66 built convertible has the early style covers. If you haven't gotten a copy of Bob Mannel's book and own a Mustang with a 289, you are missing out on a great wealth of information, it is practically the "bible" of the early 62-69 smallblocks.