Wiring for switches controlling outlets can be a bit confusing, but all I can assume is you put the wiring back exactly as found. One thing most people are not aware of, is a controlled oultet is usually split, one half is on all the time, an one half is switched. Look between the two brass screws on the "hot' side of the outlet, you will see a small "jumper" that needs to be cut or pried out when the outlet is half switched. This will leave one hot wire on one half of the outlet, and a switced wire on the other half.
I think not removing this jumper on the "switched" outlets is your problem. If not get back and let us know what you found.
Sure the outlet can be converted over to a pull string fixture, just remember that no bare incandescent lamps can be located in a closet.
See this previous post for more detail:
http://www.askmehelpdesk.com/electri...set-54306.html