Transferring Information

I work at GE Aircraft Engines and I am having a problem transferring information that is stored on a NT server which is outside of our firewall onto an inside Unix sever that places the information onto our website for the airlines to view. I have been using Unix scripts automated by cronjobs to do the job, but I found out that they are very unreliable after serveral are running at the same time. I have been told that I should switch everything to a Oracle server and use Appworx, but I want to get a few other ideals before I actually start sending a lot of time on it. What ideals do you have?