As someone who is also quite new to rabbits (Theodore is my first), I can sympathize with how hard it is to see your bun not immediately taken with his new surroundings and is not showing the personality you know s/he is capable of having! But not to fear. Rabbits, as you know by now, take time to adjust. It takes a while for them to become comfortable enough to trust you. But it sounds like you guys are doing the right things. I would start spending more and more time in the room with the rabbit, now that he’s eating. Just hang out in there and go about your business – don’t put too much attention on him. Just work at your computer or read to yourself for long periods of time. Bring some food like a healthy treat every time you come in, and he will start to learn to associate you with positive things. You don’t necessarily have to hand feed him every time, though once he’s more comfortable with you, hand feeding is a great way to bond.
As far as space goes, it is a good idea to leave him in the pen for a while until he feels secure in that area, so that he knows that he has a place to call his own. Letting him run around too much right now may be a bit daunting for him. I’d say give him a few weeks to adjust, or until he seems more comfortable. Once he starts coming up to the edges to greet you or isn’t bolting from you anymore, then you can start to let him roam a little bit and let him come to you – having more treats to hand feed will help here. Just give him space and time and soon enough you will see that wonderful personality of his blossoming. C:
Good luck and welcome to the forum!!