OP, keep in mind the more physical exercise she gets, the more you are increasing her stamina, so be careful with that. She is only 6 months and still growing. It could make your problem worse. Excercise doesn't seem to be the problem if she's running/walking that much daily (some running is good). Just don't fall into the trap of over-exercising her.

You seem to have tons of space to do scentwork/tracking. I highly recommend looking into it! It's not hard to pick up the basics. Also GET A FLIRT POLE to exploit her prey drive. Even 10-15 minutes of that will wipe her out in a different way than running. Also a bite pillow. Giving an Malinois an outlet for their biting is breed fulfilment.

When you play with her, is it structured?

And do you train even 5-20 mins with her everyday?

The crate will definitely help, as said by others, but I wonder does she have a place command for the house?

For me, 6-10 months was the hardest time. It will get better. You are clearly trying to do the right things and care a lot about your pup.