You say fecals are negative but have you had him tested for Tritrichomonis Foetus? It is a special test and handled differently at only a couple of labs. I know about this as mine have it, smelly, pudding stools are classic. Many of these cats are diagnosed as IBD, colitis etc and end up taking uneccesary meds.
http://www.cvm.ncsu.edu/docs/personnel/gookin_jody.htmlhttp://www.tffelines.com/whatistf.htmlHere are links to the most accurate information. Dr Gookin has done the research into this and if you look on her link under owners guide to T Foetus you will find good info. Dave Dybas HighgaitsPaws Abbyssinians is also good at helping. My Vet and I worked directly with Dr. Gookin on this as it is relatively new and not many vets really understand it. Sadly most dismiss it as a possiblity but it is more common than thought and getting more so. It is in a lot of catteries, shelters etc.
As a footnote, mine were unable to take the meds, so they are now 4 yrs old. and they still have bouts if I mess with thier food or they get upset but it is not often and clears on it's own. They have not had a major problem for several months. They are however contagious and will be the rest of thier lives.
I suggest you have the test, even if your vet is doubtful, but read the info first. It is tricky to get it right, do not medicate without the test as the meds can be a problem. Most cats tolerate it okay and just need to be watched closely, mine are the minority. good luck