Ars Technica (the Web site) recently had some fun generating a custom coin, which readers could mine and then redeem for nifty perks on the site, like hats on their usernames. They posted a series of articles about how they set it up; here's the main one you'd be interested in. Maybe you could use it as a guide, or a starting point for your research.
http://arstechnica.com/business/2014/03/behold-arscoin-our-own-custom-cryptocurrency/They used a Web site to create the new altcoin, including custom node and wallet apps.