There is a Shuffle! manga... actually two of them (one is the story line, the other are little storylets contributed by other artists) and a series of novels ... all in progress.
And all in Japanese.
You can order them by searching for Shuffle! at
www.amazon.co.jp or other fine export shops.
I'd say the chances of a season two is just about zero for now. The energies of Navel are focused on their upcoming series called Soul Link. It may be that we'll see an OVA or something for Shuffle! this summer. Reaction to Shuffle! in Japan from the target audience appears to be mixed.... Everyone was very excited about the set up, premise, and character design... but the climax and final arc of the series was kind of muffed by poor writing.
One of these days, these production teams will learn to put their best talent at the front AND the back of a series.