... the pain will be almost completely gone tomorrow ready to do the box squats, which will make the pain come back up again after the workout and last for a few days again and repeat, but I don't know what that means about the state of my back.
It's obviously hard to know exactly how much pain/discomfort you're feeling and whether it's above normal expectations from this type of training, but it might mean your back cannot handle box squats right now. You could be playing with fire by continuing to go back to them and repeating this cycle. Ideally you'd want to see the discomfort fall as you get more sessions in, but if it's always bad, it probably means you should back off for awhile.
If you can, go to a good PT and get some treatment on your back. It might just be really knotted up. Or you can lie on your back, get your legs up on a couch, and get a hard ball (hockey ball or similar) into your lower spinal erectors, gluteus medius, and midback spinal erectors. See how that feels after doing it for 10-15mins a day. Then I'd just lay off box squats for awhile, but still do your other exercises that don't induce the pain.
Also, I would consider box squats to be a late-season peaking exercise and not something you're using as a main lift throughout the year. I think the best course of action for your lower body compound power lift (be it DLs, pulls/cleans, or squat) is start with a high volume of full RoM reps, low-ish weight (still ~60-70% 1RM, 5-10 reps) for most of your training block, then progressively reduce the reps, raise the weight, and finally perform the supramax versions like box or quarter squats, block DL, or hang power cleans etc., so you're moving a very high load as fast as possible. These last ones should only be over a relatively brief window in your training plan - because the aim is mostly to get stronger and more powerful at these exercises without getting hurt, which prevents you from doing your sport-specific training (sprinting for you).
In regards to my hamstring flexibility, I can lay on my back and lift both legs individually 90 degrees and I stretch it grabbing my trouser sleeves and pull it close to me. So I think my hamstring flexibility is good.
I used to do single leg Romanian dead lifts using dumbbells in both hands, but I stopped because it was hurting my back. But then again I was doing it while balancing on one leg, I didn't know I could put the non working leg on the floor at the back.
Flexibility sounds fine, don't go crazy trying to stretch yourself out to the level of a contortionist. SLDLs are great and they could help a lot, especially switching the load halfway through as I described somewhere. It might address some imbalances you've got in terms of hip/glute/hamstring muscles. But definitely don't rest your rear leg on the floor though - you want to have the balance aspect.
In regards to tempo sprints, can you give me an example. Do you want me to do them every time I go to the gym.
Are you still being coached? Ask your coach if so. A good example might be [100 sprint - 100 slow jog - 100 sprint - 100 slow jog - 100 sprint - 200 slow jog - 200 sprint]^n, all at a pace where you're up sprinting on the ball of your foot, but not much faster (60-70% speed or so).
I may also incorporate long walks when I get the opportunity.
Thanks
Do that when you're retired and save your energy
. Joking - any active low-impact stuff on off days is good.
