Hi Jess,
There is a "honeymoon" stage where they are just adjusting to their new environment, which is probably what you went through in the last two weeks.

Since he was in such a neglectful situation you probably just need to give him some time to adjust to his new and more loving home. With any bird, it's always a matter of patience. It's also spring time, so they are more cranky and hormonal during this time.

Offer him some extra baths etc. to help with his itchiness and discomfort. Has he had a vet-check to see if his plucking was a medically related?

Good Luck, others will be around shortly with some more advice!