Depends on what you want.  If you want stock replacement fasteners you can buy various bolt kits from any Mustang parts house...I recommend Steves Mustang Parts.  I bought a complete body kit for ours and am pretty impressed, even though I'm sure it all came from Won Hung Lo. 
These kits have the proper finish and bolt type to replace most of the factory fasteners.  For the engine there are a number of sources out there, like ARP who supply high quality, original finish or stainless depending on what you want.  Summit Racing is a good source for such items.

A good source for hard to find or special fasteners is Fastenall.  They like to sell in box quantities but some stuff is sold in small lots...just gotta ask them.

Hope this helps.

BB

If you need the hardened bolts that have the integral flanged head, McMaster Carr or monsterbolts.com are good sources.  McMaster Carr is good because they have tech drawings for every bolt.

My rule (pretty much 100%) is never to use hardware store bolts if at all possible.  Tractor Supply is a really cheap source for grade 8 hardware if you just want a plain old bolt.  They also carry some flanged head stuff but it is way expensive.