Find That Book

...This might be Firekeeper series by Jane Lindskold, but if so I think you may have missed some of the earlier books.

The main character, Firekeeper, is female, not male, and is raised by sapient wolves; overall, the series is about her journey to develop and discover her identity as she tries to balance her human origins and her wolf upbringing.

There's a side character, however, who meets a lot of this description - Derian has a gift for horses, he does have an adventure over the course of several books that involve discovering magical gates and surviving a magical plague that causes him to develop some equine features. He didn't live with an older couple that matches your description, but he spends a few days or weeks with a couple like the one you describe; they are horse breeders and he's introduced to them because of his own gift.

Derian initially hates the physical changes in himself and regards himself as monstrously deformed, but eventually comes to accept them as a reflection of his power and his values (he could have sacrificed his horse-communication talent and retained a fully human appearance), and finds love.

The first book is Through Wolf's Eyes, and it was published in 2001. The bulk of the stuff you remember (if I'm right about it being this series!) starts with the fourth book, Wolf Captured, which was published in 2004.