How many times a day do you feed him? Yellow bile usually means empty tummy so you might want to spread out his meals more. Like if you feed him twice a day, feed him 3 times a day.
For runny poop, boiled chicken/rice is good but since you can't boil chicken, pumpkin is another good alternative. But be sure to get the organic 100% pumpkin like this one:
http://1w6j8040ci6b2pkd7329rcf7.wpen...t_pumpkin1.jpg
As for the peeing... it sounds to me that he is in fact marking. Is he still in training? Perhaps try belly band to save your furniture/house from the pee?
