First thing you need to do is relax. He will do great. My son is going into 4th grade this year and is still as mobile as when he was in 1st. Go to the IEP and take with you the education matters books for school personel that you can order free from this site. Ask for PT/OT. He may need extra help or time with some subjects, but remember that you can add or delete anything on the IEP at any time. Get to know the teacher and email often. Volunteer for class functions. Our school walks to alot of fieldtrips, so I just drive him. He just might fall or get lost, but so will all of the other kids.
Education Matters: A Teacher’s Guide to Duchenne Muscular Dystrophy, and Adaptive PE: A Teacher’s Guide to Duchenne Muscular Dystrophy
Our son has just started full-day kindergarten in a school that goes to 4th grade. Like you, we were worried about his safety in this bigger place with bigger kids who are just banging around as kids do. We insisted that he have a one-on-one on the playground and in PE, as well as someone to help him on and off the bus. It sounds like your son would benefit from the same. Additionally, Gus has PT and OT, and he is able to go to a therapy pool nearby for swimming each week.
Remember that it is federal law that the school meets the needs of your son in "the least restrictive environment" possible. That means he shouldn't be pulled into a special room unless it's absolutely justified. If the school can't meet his needs, then the district has to pay for an outplacement, which usually costs $75,000-$125,000 or more. Because of that, it is in the school's best interest to meet your son's needs.
Also, by law, your son has to have a signed IEP - take the unsigned copy to his doctor, to your local MDA chapter, read it against PPMD's document (http://www.parentprojectmd.org/site/DocServer/EdMatters-TeachersGui...)...the important thing is that you DON'T sign it until you feel comfortable.
All the best as you go through the IEP process!