The listening skills issues in class and the repeating of instructions make me wonder how well your son hears in noisy environments. My son had multiple ear infections when he was a toddler and pre-schooler, and has been diagnosed with an auditory processing disorder, dyslexia and mild ADD. He has big problems understanding accents, hearing in noisy environments and remembering multi-step instructions. He can organize a paper pretty well as long as he understands what is needed.
My son benefits from receiving extra time on tests and gets written notes for some high school classes. He used to use an FM system to help isolate what the teacher is saying from the ambient noise. His gifted classrooms were usually pretty noisy.
Another really helpful accommodation is a website with high school assignments, due dates, and a list of what is missing or has been turned in. I wish all the teachers would use this system, but many do not.
