I don’t think you will ever get 100% poops in the litter box. Poops are easy to sweep up though.

Neutering and maturing should help a lot.  I struggled with my first bunny and had to wait out the “teenager” stage until I could get her spayed and then a few months afterwards when her hormones settled and she became more settled and used the box as she should.  She still does poo outside her cage to mark- but it is easily cleaned- and so preferable to the pre-spay peeing outside the box that it does not bother me too much.

After going thru one baby bunnyhood- I have only adopted already spayed and neutered adult rabbits since then- it is a trying and frustrating time.  It is hard to see your cute loving bunny that was so “cuddly” and personable as a baby turn into a teenager that growls, bites, boxes and stomps, and it is hard not to take it personally and feel hurt.  Even though I understood why Cotton was doing the behavior (hormones) it still was upsetting to me.  But getting her and myself thru it by limiting her areas to cleanable ones and patience to wait til the spay, the anxiety of spay and recovery, and then waiting for her to settle was worth every moment. 

Things should improve once he’s been neutered. There may always be a few poops dropped outside the box, but that’s really not a big deal. A hand-vac is great for picking those up, or if you’re not squeamish (like me) you can just pick them up by hand… ;o)