Sensitive tummy

So my rabbit has troubles with not eating all of his night feces. After switching his food to pure timothy hay and timothy pellets, an antibacterial treatment, and numerous visits to the doctor, it has been determined that he is just particularly sensitive in the gut flora. It's unfortunate because I've been experimenting with greens and veggies in moderate doses but I haven't really found anything consistent that doesn't set him off. I want to give my bun more food than just timothy hay and pellets though so that he can have a varied diet. Does anyone else have a sensitive rabbit, and if so how do you keep them regular?

Are the cecotropes formed normally(before they get stepped on) or are they mushy at all when they come out? How much pellets do you feed and how much does your rabbit weigh? Excess pellets in the diet can cause an overproduction of cecotropes, which may be left uneaten. Have you tried reducing pellet amounts to see if that helps?

Is he overweight, could he possibly have arthritis or dental problems, or has your vet ruled these out? Overweight and arthritic rabbits can have problems reaching down there to eat their cecotropes, so they may remain uneaten. Dental pain can sometimes cause a rabbit to not want to eat their cecotropes or can cause them to eat less hay resulting in mushy cecotropes developing.

http://www.bio.miami.edu/hare/poop.html

I give him about two handfuls of pellets, and I refill it when he runs out. The vet says that he is a good weight for mini lops so I will try reducing his daily pellets. What is a good proportion for a mini?

Edit: it is almost always fully formed (though he usually steps in it before I can find and clean it) though it has been mushy a couple times.

It could be too many pellets as previously suggested. The general accepted measured amount is 1/4 cup per 5 pounds of rabbit daily. So if your rabbit weighs 2.5pounds, you feed 1/8 cup or if it weighs 10 pounds you feed 1/2 cup. It's best to know your rabbit's weight, but wikipedia is telling me that purebred mini lop boys are usually around 4.5-6.5 pounds, so 1/4 cup daily would suffice. Bandit weighs 6.5 pounds and I only feed him 1/4 cup daily in a morning and evening meal.

Presuming all other health problems have been ruled out as the cause and he was found to not have any dental issues, I would try to see if it is diet related. He may just be sensitive to too many pellets in his diet. Not sure exactly how much two handfuls is(if that is the total amount fed in a day), but you could try the 1/4-1/2 cup a day depending on your rabbits weight and exactly how much you are feeding now. I would at least reduce the amount by a fourth of what you are feeding now to see how that goes, or even reduce pellets by half if the mushy poop/excess cecotropes is a big problem. If the problem is really severe, removing pellets completely, temporarily or even permanently, may be necessary. The important thing is to ensure your bun makes up for the reduced pellets by eating a lot more hay and always has access to hay. You also want to monitor his weight to make sure he stays at a healthy weight. Then once this is resolved for a few weeks, then you could gradually try adding in veggies, starting one at a time and in small amounts.

http://www.sawneeanimalclinic.com/downloads/chronic_intermittent_diarrhea_in_rabbits.pdf
http://www.veterinarypartner.com/Content.plx?P=A&A=3012

On the flip side, if he really is sensitive to greens/veggies and the problem isn't with the pellets, there is nothing wrong with a pellet and hay diet. Plenty of rabbits do fine and stay healthy on this diet. Variety in the diet is more of a human want and not generally necessary.