any suggestions on the best way to spend 2 & 1/2 days in Takayama ?

Sure, take a day trip to Shirakawago. I believe the bus between Takayama and S-go runs year round. You will need footwear for snow and slush (which likely applies to Takayama also).

There is an onsen bath at the Green Hotel and it is open to the public. Gero Onsen is not far south by train from Takayama.

Have a bowl of hot Hida ramen soup. IIRC, the spot I would take you to for this is on Kokubunji Street, on the left just across the river when heading from the station. In the same block as the restaurant with the bull statue but on the other side and closer to the station. Beef in the window and for sale on one side of the shop, a few wooden tables on the other side. Very informal. Good stuff.

Then there are the usual attractions in Takayama. Hida no Sato if you don't go to Shirakawago. Takayama Jinja. There is a ski resort in the mountains to the east.

http://www.jnto.go.jp/eng/location/rtg/pdf/pg-409.pdf
http://www.japan-guide.com/e/e5900.html

If you have any interest in glass or interior design from the Art Nouveau + eras, consider visiting the Hida Takayama Museum of Art.

Do go to one or both of the morning markets, not necessarily to buy anything, though perhaps you'll find a nice vacuum packed traditional local pickle to take home, or some sesame or miso candies... but to enjoy the visual feast of familiar and unfamiliar items on sale. And there are tasty treats you can buy to try as you go...
Some pics / info:
http://www.kaveyeats.com/2012/12/miy...-takayama.html
http://www.kaveyeats.com/2012/12/owa...-takayama.html
http://www.kaveyeats.com/2013/01/mitarashi-dango.html

You may also enjoy visiting some of the shrine floats in their special sheds. And the shrines themselves. And there's a pretty temple walk you can take. And of course, walking through the pretty preservation areas, to appreciate the traditional wooden machiya and many have little shops, cafes etc within.