Please take some time while you are working on it to clean up and fix the rest of the wallet, as it is right now the linux wallet expects "coin.conf" in the same working dir as the executable and assumes that is the data directory as well.  Its nothing that can't be worked around if you have a little experience, but its kind of annoying.  If I were you guys, I'd take the latest Bitcoin 0.9x code and use that as a base, and bolt the scrypt algo on it.  But that requires a little more time and skill as well as the switch to autotools.

Just my 2 satoshis.