I did find that kids couldn't make the whole 90 (especially early in the year). Break it up a bit. Do a theory lesson in the middle. Have them get up and move, even if it's just relocating to an ensemble room to do sectionals for 20 minutes.
Try to get the kids playing on the "off" days. I know one school that does morning full-band rehearsals on the days they don't have band class, and morning sectionals on the days they do. When I had this schedule I tried to assign a recording of some sort every class day. Most of the kids don't work ahead, so if it's due Wednesday they'll do it Tuesday night. Make it something short and simple so you aren't grading forever.