My horse started out not liking being touched -- he just "sucked it in" (amazing how far!). He evinced some mildly threatening behavior, but nothing like the kind of fighting you are describing. If your horse really is unsafe, have an experienced horseperson work with him or leave it for a vet. If one vet can't manage it, get someone who can.
I start by leaning against his flank/haunch (defensively so as to not get kicked -- close in can be safer, and watch that body language!!! And wear a helmet, etc.) while stroking him on his back and butt. The stroke must be firm enough to not tickle, but still gentle, slow, and soft. This is just basic grooming and petting, like you do every day.
I progress to the under-dock area (when he lifts his tail, he is enjoying it and submitting), then between the hind legs (soooo soft!) first from behind, starting at the hock and then up to the leg join, and then the same from the front. When he accepts that, I slowly move to the outer sheath. Just being able to pet the outer sheath and let it rest in your hand is a major step. I like to do this while my horse is eating hay or grass after a ride.
That progression can take a few minutes or several weeks depending on the horse.
When the horse is relaxed enough for me to get serious, I break out the old KY Jelly and start another progression from just barely touching the sensitive stuff on in. I've had my boy for nearly two years and only last week was I able to really get "into it". Putting a lubricant on the night before can help soften stuff up so it doesn't hurt to pull it off.
Take advantage of his letting down to pee -- don't stroke or clean at first, just let it rest against your hand or try a gentle hold. When he is comfortable, try a gentle (but not tickly) stroke with the back of the hand. Only then try to gently remove some dirt.
This sounds like a sex manual. How old did you say you are?