Hi Erika,
My cat Rocky was rescued from a hoarding house when he was a kitten. He went to the local shelter and I adopted him there. He was the shyest cat there but he was so beautiful that I fell in love with him. He was very standoffish for awhile and afraid of everyone, including me until I drew him out. He also has had behavior issues but not scratching. I'm sure there's a way to get past it. I'm thinking it is likely because of his recent situation and all he has been through.
Thank goodness you found him. His room sounds fabulous, like kitty heaven.