The problem with your Maine Coon's digestion could just be down to a food allergy or sensitivity to any additives or by-products in the food. If the food has both chicken and fish it in try a food with just one protein source. Or alternatively you can make your own cat food. I always recommend raw meats (chicken, fish, lamb, rabbit, duck, or venison) with steamed vegetables like green beans, peas, or carrots and potato instead of rice. Much easier on the digestion. Also, a must is adding 250mg-500mg of Taurine (amino acid you can get at a health food store) per cat daily.
If you're in Ireland or the UK check out my video in the Videos section of this website for a great cat food recipe using a dog food and modifying it. If you're in the States there's an excellent cat food put out by Burns Holistic Pets. Visit www.burnspethealth.com for a stockist.
As for free feeding, that should be easy to remedy. You just put the food down in the morning and again in the evening. Eventually they will catch on to eating at set times. Especially if the food is tasty, they'll want to eat more at every feeding.

Hope this helps. Contact me at jessi@tailwaggers.ie for any other questions or concerns