D.B.
What you need is a craniofacial team to work with you and your child. Take him to a children's hospital that has a cleft palate, maxofacial cranial department. Get an appointment with the ENT there and tell him or her that you want a nasal endoscopy done for your son. One that has a television screen to look at his entire structure. Tell them you want him to be assessed for the possibility of a submucous cleft palate (don't let them tell you that because he doesn't have the telltale bifid uvula, that he doesn't have a submucous cleft - it's not true), velopharyngeal insufficiency (VPI), deep pharynx, etc. Without a nasal endoscopy, they have no idea. Bring all this up - tell them you want to rule it out. If your child has been in speech therapy for a year and still is not understandable, there is a structural problem or the structure ACTS as though there is a problem. Some VPI can be functional rather than structural, but speech therapy has to be done regardless. And some of these issues, like VPI and resonance problems, are beyond the understanding of regular speech therapists.
How do I know this? Because my own son has a submucous cleft (without that bifid uvula). They missed this diagnosis until he was 4 years old. He also has a short palate. And he had such bad functional VPI that he could not say any consonants - only vowel sounds. His resonance was also a mess because of hypernasality. An ENT tried to get me to let him take out his adenoids - if I had, it would have wrecked ANY semblance of normal speech he would ever have - you can't take the "roof" off of a shortened palate when there are nasality issues. Because I wouldn't let this ENT bully me into surgery with no diagnostic testing to back up his reasoning for removing the adenoids, my son has decent speech today. I kept going until I found an ENT who would do diagnostic testing. THAT was when we found out about his cleft.
Adding here about this issue of him sounding like a deaf person, that may possibly be HYPOnasality. That's a hard diagnosis too, like the VPI. Your regular ENT or doctor or speech therapist cannot diagnose this or know how to fix it. You need the big guns, Alisa.
You must do your own research and be your child's advocate here. DEMAND diagnostic procedures to help rule out structural abnormalities. When you have a real diagnosis, change speech therapists for someone who has dealt with your child's issues before. I know it's expensive. I know speech in school is free. But if I had just used the EI and school therapists for my son, he'd still be snorting his sounds out and no one would understand him. I met a young man in his early 20's who sounded like my son before we were able to get the snort out of his last consonant (an "s"), and I cried when I left him. Obviously, no one helped him. His resonance was SO nasal, and his consonants were SO sloppy, I could barely make out his speech, and believe me, I've had LOTS of practice.
Sending you strength,
Dawn