First some possible medical causes:
The vet might have missed something. Irritated bowels cause runny, frequent, and inappropriate pooping. It can be caused by gram-negative bacteria, whose excretions are poisonous or at least irritating, depending on the serotype. A fecal exam is a lab test that spots those foreign, unwanted bacteria and fungi.
Something stuck in his digestive tract, like a sharp bit of debris that iguanas typically eat when the find them. I had an ig who began to fail to thrive, and had the runs, when he had a dime welded to the inside of his stomach. They called it zinc poisoning I think. But it also directly irritated and slightly damaged that small circular part of his stomach. Stomachs normally protect themselves from the acid with a thick layer of extra stiff mucous.
The death of an ig's symbiotic hind-gut fermentation flora and fauna causes various upset throughout the lower bowels, and possibly the whole digestion system. There are various things that reduce that population. Insufficiently high basking temperatures, a compulsion to avoid basking (by other illnesses or stress), viral and bacterial infections, low eating, dehydration, and probably stress, are some that I know of and had experience with over the years.
Behaviorally induced bad poop habits can be caused by problems with the habitat, such as any kind of change. Sudden bad eel ing toward their humans causes it. A sure sign of this cause is when they poop on your pillow or poop on their own soft bed.
A child, cat, dog, etc. close to the glass, tapping/knocking on the glass to try to get a reaction, staring in at the ig, typically cause great stress, and bad pooping is a common and biologically benign result. It's caused most likely from people experimenting with your ig when you're not there. Anyone, you'd be surprised, can do that in my experience. Not benign for you of course, and not to say that a very long spell of this can't be harmful, such as behavior-induced dehydration or malnutrition. skinniness and depression are signs of that, but it would be months before those signs became apparent.
I agree with you that your ig has a significant problem, and needs a blood test, fecal smear lab test, and x-rays to screen out obvious causes. The high expense is a necessary part of responsibly keeping a pet iguana :-(
Don't let your vet substitute the fecal test with a look-see through his own expensive microscope. He can only see large pests like giardia and tapeworm ova, no matter what he says. He may be an excellent histologist, but he still can't morally practice that on your ig's possible problem/s. Several of the pests need to be grown in a lab on petri dishes to be able to identify them.
I've never heard of any vet who has a cell-growth lab setup, nor any who said they had the skills that lab techs gain over time.
If your vet has even a moderately good scope and all the slides, lights, and dies, yes he can see bacteria at 600X, but he can't scan them and be sure he locates and accurately identifies the malefactors.
If your vet won't do those tests, you ig needs a less self-inflated new vet.