Because you disconnected the wires to the fuel guage you have now broken the electrical circuit for the fuel level system. It all ties in with the fuel level sensor so you will have problems.

I had the same issue and there is a resistor that can be setup to go between the 3 wires which use to be connected to your fuel guage but I really couldnt tell what Ohm resistor it should be.

In the end I cust of the top of the fuel cap and placed it back in the hole still connected with original wiring then put my custom RSD cover on the top of the whole thing you wouldn't even notice and the low fuel light still works correctly now.

There is a whole post which I put on this forum pointing out the details sometime back..........

http://www.hdforums.com.au/Default.aspx?tabid=71&forumid=24&postid=361927&view=topic

I took the globe out of dash on last harley, easy job solves problem. I always know exactly how far I got left as I always click my b trip metre when I fill up