Minecraft Server connection problem

Hello fellow minecrafters,
I recently downloaded and ran a server.exe. That worked great.
I then downloaded minecraft server.jar, and used a .bat file to run it. That worked just fine.
After that I ran the server.jar, and used bukkit and added some plugins. It worked phenomenally.  Until I decided to install the physical shop plugin, (which allows users to use chests to make shops.)  I installed it and ran the server, then when I went to login to the server via minecraft. It got stuck on the login, and either it stopped working, or it would give me a screen similar to the failed to login: bad login screen. But it had a file directory for a random file, and some extra HTML code under it.
I completely reinstalled minecraft, and even deleted the .minecraft folder.

It also may help to know that I used the manual download for the 1.6 update which was provided in 1.5.2. But now I have no idea how to get to the real 1.6 launcher.
So, if anyone has had this experience. Or they know of a solution, or can direct me to an article or someone that can. It would be much appreciated.