Yes, the back can hurt, if there is bowel inflammation.

Two years on doxy is enough to kill off all the beneficial bacteria and allow the nasties to take over.

Your son may have Crohn's.
I don't know of any multivit high in D.
I don't know of any multivit with probiotics.

The cephalexin will continue to kill off beneficial bacteria.
Your son may have Candida --this comes when beneficial bacteria are lost. Probiotics do not kill off Candida...this is a fungal organism and hard to get rid of.

If someone is low in D a high dose Vit D3 is usually given
He would need at least 2000-5000 IU daily to bring levels up and then perhaps 2000 IU daily after that. If he is really low, he needs even higher doses.

If the whole GI tract is inflamed I would start on EFAs NOW.
These fats rebuild the GI tract. I have a thread here on the subject. (some foods have them in it now, so you can get them that way...peanut butter, eggs, mayo etc.).
http://neurotalk.psychcentral.com/thread6092.html

This health crisis did not happen overnight, and it will not heal up overnight either. Doctors can give you drugs for symptoms, but they will not build new tissue, where there are
ulcers or inflammation.

A multivitamin is not enough. A multi is for daily use (as a replacement for certain foods). When drugs destroy your status completely, a person needs higher amounts.

Why is your son refusing to go to the bathroom? Holding it?
Is this about school? People with dysbiosis (nasty intestinal bugs) have very foul smelling stools. This may cause ridicule at school, and also be offensive to your son. Some boys will not go at school because there are no doors on the stalls, and they are subject to bullying in the bathrooms.
Also infections in the bowel, irritate the anu$ (there is a blocking filter for this term here), and infections/sores/ or fissures/ or even a fistula may occur. Pain in this area results in stricture of the sphincter and makes things worse. Hence, the patient avoids passing stools. This "leakage" may be from a fistula..and should be examined ASAP.

I guess you will have to prioritize things. Get the GI straightened out (it will never get better while using antibiotics-- only worse).

Chemar here has threads on how she healed her son's Crohn's disease...I'd PM her and find those links. It can be done but it requires effort and homework, and money since many of the most important things are NOT covered on insurance.

I would start looking for a holistic doctor who can perhaps put things back together for you. Traditional medicine does not know how to do this, as a rule.
I'd check and see if this spot has a holistic medical department:
http://www.hurleymc.com/

I found several hits for holistic medicine Flint on Google.
I'd seriously suggest it. The doctors who do the pyroluria testing are typically DAN doctors (Defeat Autism Now), but some others know about it too.

This is a huge problem.... so take it one step at a time.
Try to make food changes slowly, since people resist food changes (food is often a comfort).

And start researching gluten intolerance. Many many chronic GI problems go back to it. The stickies on our Gluten forum are an excellent starting place.