Welcome and congratulations on your new bunny!
It can take a little time for their trust to build, being a prey species. The “floor-ignore” technique can help which is basically, hang out with them down at their level and let them approach you. Keep yourself occupied reading, watching tv, browsing the internet etc and just allow then to come over to say hi, or jump all over you. It’s not unusual for rabbits to dislike being picked up, even if they coped with it okay as babies. Often as they mature, they’ll become more independant and not want to be held. So snuggles become you lying on the floor and them keeping their 4 feet firming on the floor but they may enjoy nestling in next to you.
The House Rabbit Society site is a great resource and a site worth bookmarking! This article may interest you. http://rabbit.org/first-few-weeks-in-a-new-home-2/
It’s great that he his eating from your hand.
Regarding his food, it sounds as if the rabbits were on a pellet/seed/grain mix? These are not ideal as rabbit will tend to eat their favourite parts and not get a balanced intake, which the pellet is supposed to provide. Overindulging on the fatty seeds or high carb grains can let to their gut flora becoming unbalanced and then messy poop. A plain pellet feed is more suitable. Corn is also problematic and is thought to lead to blockages.
If there is pellets in the mix, try give only those. If you prefer, you could then slowly transition him onto a more suitable plain pellet feed.