Godaddy WordPress Reinstall Issue

Hello everyone, last night I was going through and re-installing my WordPress on my Nitrodesigns.net hosting account on Godaddy, the “root” domain, since the website was unstable I figured I would just reinstall it and start from scratch. In doing so, many of my websites that I have through that hosting account are having issues. For example.. this website I am working on..

http://nitrodesigns.net/fastco/wordpress/

.. if you click on any pages it brings you right back to my main root page for some reason.

Also, on a website that has been fully up..

http://www.djshaw60.com

…none of the pages appear now, they come up blank.

Then on some of my websites, such as..

http://www.evanbeaulieu.com

..all my pages except the ones generated out of wordpress code (articles page) show up fine.

All I can say is I deleted the wordpress files last night on the root hosting account and re-installed it. Somewhere in doing that I have screwed this up big time.

If anyone could please help me with this, that would be great! Thank you.