Nine Month old w/ stool througout gi tract; including small bowl - going on 4 weeks

I have a nine month old who is clincial considered mildly low tone.  He has a variety of medical issue; all of which he is handling extremely well; and do not interfere with his daily life.  Gastronenterology wise, he was diagnosed w/ grade 4 acid reflex at two weeks old.  He was scoped at 9 weeks and had no abnormal findings; other than some irration & acid reflux.   He also has swallowing / oral coordiniation issue and therefore everything he eats / drinks is thickened w/ simply thich to honey consistency.

At the end of August our son began turning colors when he ate; it would appear as if he was bearing down / pushing down but rarely was a bowel movement involved; we conducted a swallow study; to which he did not pass; however none of these episodes  occurred during the study.  His OT witnessed a episode and advised holding off on baby food until speech / drs give OK.  dr's gave OK; speech therapy got involved and slowed down food; we began adding texture etc.. and he was progressing great for  about a month.  recently the episodes have started again; only are much more manageable as if we put him upright (i.e. exersaucer) he can typically finish his meal.     During the month of October, his belly got extremely big.  He got a belly x-ray and stool was everywhere, including the small bowel.  concurrently, he tested positive for c-diff.  approx 11 days we re-evaluated w/ another x-ray and repeat test.  the x-ray was still somewhat concerning considering the amount of stool but it was out of the small bowel and less than the previous X-ray; when the test came back for c-diff it was still positive so we proceeded w/ another, different antibiotic for three days.  Approx 2-3 days after completion of that he was doing great then his belly got huge again; We did a another x-ray and  sent stool out for a culture & c-diff.  The x-ray came back and we are back to where we started w/  a huge huge amount of stool.
Are there any ideas out there about other things we should be looking for?  Ways to get rid off all the stool.  Our concern , as parents that w/o getting the old stool out how will the bacteria get out.  Our son is consistently having bowel movements 2-3 times a day; sometimes up to 5-6 times and range from mushy to slimy; prior to all the feeding issues his  bowel movements were always softly formed (think play-doh) which we attributed to the simply thick so; we are also very concerned about what is making so much stool in his body.  Any ideas that can help or thoughts of things to research / ask or doctors about are greatly appreciated