Stay. In. The. House.
To do otherwise is legal abandonment of your family (and son!) and will hurt you terribly should you separate or divorce.
Also, it is much easer to build a good marriage if you're in the house living together. It's more difficult to build the marriage if you don't spend lots of quality time together.
You say you have fixed everything she thought was negative about you. That is a good start. Do you know about the concept of the Love Bank? Do you know what her top Emotional Needs are? Are you doing things to meet her top ENs every day? Because you could be taking her out to dinner and ball games and movies and roller skating... and if Recreational Companionship is at the bottom of her list you are totally wasting your time, energy, and money. If her top EN is conversation you'd be better off taking a slow walk around the block or sitting on the porch chatting and asking about her day, her dreams, her feelings.
So... find out what her top ENs are and focus on those.
Are you familiar with the concept of Love Busters? Read up on them and eliminate them from your behavioral repertoire. Angry Outbursts are easy to spot, but Disrespectful Judgments are slippery little beasts and take a lot of work to get rid of. Independent Behavior is a tough one for many people. It's vital that you not commit ANY love busters because a LB is like a hole in the bottom of a bucket. You can try to fill the bucket by meeting ENs but the hole (LBs) undoes all your work faster than you can fill it.
When she says she feels nothing for you, she probably feels something for someone else. Have you ruled out the possibility of an affair? Do you have access to all phone records, cellphone records, credit/debit card records, etc.? Do you know where she is and who she spends her time with? Don't ask her, just look and find out for yourself. Check her email (especially the sent folder). If she's not in an affair so much the better. But if she is, you need to know because things cannot improve between the two of you if there's a third person involved.