Yes your numbers on a box squat 3 rm will be a lot lower than your 3 rm regular squat. At least for me. I hit 550 box but reg squat in the 600's. On speed day the way i understand it is you progress up 50, 52.5,55,57.5,60 % but you can do it how you want it. But doing the heavy squats after speed I wouldn't do. I would put those heavy squats on max effort day. The reason is there is not as much recovery time between speed day and max day as max day to speed day.