cat w/behavior problems

Question
I'm looking for insight on a complex issue concerning one of my cats. I'll include all info that might be relevant, so my apologies for the length. Any possible insights would be appreciated, and thanks in advance for taking the time to read this.

THE SITUATION:
We have a cat named Flex. He is just about 6 years old, and he has this horrible habit of pooping on the floor instead of in the litter box. It's only his poop that doesn't make it to the litter box, though we did have an incident about a year ago when he was peeing on the floor too.

THE BACKGROUND:
I'm pretty sure this is not just a behavioral issue. Flex was an extremely healthy cat until an illness he suffered 2 years ago. We had adopted a new cat who had fleas, so we treated Flex with an OTC Hartz flea medication. Big mistake; he got extremely sick with something shortly thereafter and was hospitalized overnight with the vet and given antibiotics. He slowly recovered but never really seemed 100% since that incident. A few months later, the pooping incidents started. They would be in various places around the house, and sometimes they had blood in them. We took one to the vet for analysis but they couldn't find anything wrong with him and said it was probably irritable bowel syndrome but no tests were run to say this conclusively.

So, we pretty much just put up with the pooping habit. We moved to a new house, and it stopped for several months, but then he started it up again. When we moved again several months later, again the pooping habit stopped but then started up again.

We saw a new vet, who again pronounced him healthy and seemed to think the pooping was related to irritable bowel syndrome. They gave us a special type of cat food with "rabbit and green peas." We started feeding that to him with no effect. But something the vet said at that time struck a chord...that maybe he wasn't using the litter box to poop because he associated it with pain, and he was running off to other places because of that association. So, we took the top off the litter box (it's a covered one). Immediately, the pooping stopped for about 4 months. We weren't sure whether it was the litter box or the effect of the special food (which was $25 a bag).

Then, the pooping started up *again*. Hubby put the top back on the litter box since that was no longer helping, and the pooping continued. Then, we ran out of the special food and since it was so expensive, we concluded that it wasn't worth the money since the pooping had started up again. We switched back to an organic Whole Foods store brand of cat food that he had been eating up until we started the special food.

Hmm...the pooping stopped again immediately after we quit using the special food. It hasn't yet started up again, but I am completely baffled by this issue and the veterinarians we've seen are no help at all in helping me understand this.

SUMMARY:

Pooping starts a few months after post-Hartz flea medication illness.

Pooping stops when moving to new house, starts up again after a few months.

Pooping stops when moving to new location, starts up again after a few months again.

We start special diet cat food and remove top from litter box, pooping stops for 4 months.

Pooping starts up again, litter box top goes back on to no effect.

We discontinue special food, and pooping stops.

All the while, the poop does have occasional swirls of red blood in it...though vet claims there's nothing wrong with him except possible irritable bowel syndrome and no solutions have been offered.

QUESTION:

I figure it's only a matter of time before he goes back to pooping outside the litter box. Do you have ***any*** insight or ideas at all as to what is causing this problem or what we can do about it??? :-)

Answer
Hi Krissi!  THANK YOU for being so very clear and detailed as to what's going on with Flex.  Your details have helped tremendously!
Any over the counter flea control is horrible and dangerous.  I'm actually constructing a petition to get the stuff off the market.  You have no idea how many pets have died from these otc products...Hartz being the #1 worst.  You are so very lucky that Flex made it.  You wouldn't believe the kinds of things these products cause...siezuring especially, and death.  Flex must be one tough guy to have made it through!
I don't think I'm personally satisfied with what you've been hearing from the veterinarians Flex has seen.  Irritable Bowel Syndrome is a possibility here...I have a cat that has this very seriously and there are some similarities in Flex and my Niko's symptoms.  The thing is, IBS is not just left go.  What IBS is:  The intestines become very raw and inflamed.  You may see some vomiting during a flare-up, as the intestines and digestive track are so swollen they will not allow food to pass.  In most cases, food will be allowed to pass, but digestion and defecation can be quite painful.  The more the intestines have to work, the more raw they get, resulting in bloody stools.
IBS is treated with a steroid.  It reduces the inflamed tissue, which allows digestion to take place without all the friction and irritation that occurs when swollen. A steroid injection is usually given once per month to keep the flare-ups from occuring.  I had tried those prescription diets with my Niko, but it seemed to only make him worse.  I am feeding him Solid Gold brand food...a German food that I feed all my animals, that is 100% natural with no carcinogen preservatives and no by-products.  I have seen such an improvement with this brand of food.  Maybe this would help Flex?  
There is also a syndrome called Mega Colon.  Mega Colon is a disorder that literally causes the nerves and muscles in the colon to become paralyzed.  This may be constant, or it may be sporatic.  It may be apparent for 5 years straight and not happen again for two more.  It's a very odd illness, but is actually quite common.  What happens is, since these muscles and nerves don't work properly, defecation is very painful.  Often times, the cat becomes constipated, or diarrhea may occur.  It's one extreme or the other.  Because of the constant stress on the colon, irritation occurs, which leads to blood in the stool.  More times than not, defecation will occur outside of the litter box, because as you said, they associate the litter box with pain.  Mega Colon usually occurs in older cats, but the reason why I would definately feel as though this is a possibility with Flex is because you mentioned that this had occured after the Hartz flea medication.  These products attack the nerves and muscles...which could no doubtedly lead to Mega Colon.  The treatments for mega colon are Cefulac Syrup and Cisapride.  There really are no procedures that diagnose Mega Colon.  It's diagnosed through the symptoms that the cat is experiencing during defecation and the medication is prescribed.  It may be a good idea to mention this to a veterinarian as they may prescribe the medication to try it out, which may have some beneficial consequences.
I wish I could be of more help!  I will have to agree with you...a behavioral problem does not equal bloody stool.  Blood in the stool either means that there is an irritation (like IBS or Mega Colon)or an intestinal infection, or that there is an intestinal parasite like Coccidia present (but you mentioned that there has been fecal testing done, so we can rule this one out).  All of which are treated with medications.  So, basically, Flex needs medication and a veterinarian that will actually diagnose and treat him instead of giving you the run-around.  Flex seems very important to you and you both deserve a clear answer as to what's going on with him.  I really wish I could be of more help and I truly hope you find all the answers you're looking for.  Please, if you have time, keep me posted and I will keep Flex in my thoughts.
Good Luck!
Hilary