As far as I know, stone shards are only byproduct of crafting stone tools. You can repair stone tools use cobblestone blocks also, so shards are not a big deal.
All metal tools require a smeltery and a tool cast of the tool part you want to make.
More info in the wiki: http://tinkers-construct.wikia.com/wiki/Tool_Crafting
Makhovitz - Thanks for the reply. Ok on the cobblestone. I did not see that in the wiki.
I will start reading up on how to make and use the smeltry.