Porto Seguro is separated from Arraial D'Ajuda only by a short boat ride across the river, so essentially you can see both, as well as taking the local bus or walking the sand to Trancoso. You can take a comfortable overnight semi-leito bus on Aguia Branca from Salvador, arriving at 7am in Porto Seguro, for about R$90 one way (vs. R$289 by GOL flight). Porto Seguro and Arraial D'Ajuda have beach clubs that have music as well as restaurant service and the usual chairs on the sand. In Porto Seguro, see the site of the discovery of Brazil, and the little stalls of native Indian crafts.
Morro do Sao Paulo, while beautiful and worth spending time in, will not easily break up your journey. Transportation is easiest and cheapest from Salvador and retuning there.
Ouro Preto, as well as some of the other Colonial historic cities in the dramatic mountains of Minas Gerais, like Tiradentes and Congonhas, are lovely. There's a fun steam train between Sao Joao del Rei and Tiradentes.
I also like Belo Horizonte, which has lots of great bars and restaurants (savory Mineiro food and locally made cachaca), and one of the best Sunday feiras I've ever been to. Here are some other opinions and suggestions for B.H.
http://travel.yahoo.com/p-reviews-481683-prod-travelguide-action-read-ratings_and_reviews-i-sortorder-3