Back in 2000, the RAS published an article about Pepys’ astronomical activities in their magazine A&G.
You can read it online here: http://adsbit.harvard.edu//full/2000A%26G….41d..23W/D000023.000.html
As I understand it, telescopes of this era were always measured by focal length, rather than aperture. So “12 feet” does indeed refer to the length (similarly, Herschel’s “40-foot” telescope had that focal length). The instrument apparently cost Pepys the small fortune of £9.
The article also points out that Pepys’ activities with optical glass went beyond astronomy… 26 May 1667… “I did entertain myself with my perspective glass up and down the church, by which I had the great pleasure of seeing and gazing at a great many fine women…”