Hi Waheed, it sounds like your not having much luck at the moment.

There's a strong possibility that you may have melted some wires inside either the main control harness or the throttle cable wiring.
If the +5V feed on the controller harness was not present with everything plugged in, but it returned with just the throttle disconnected, the short will hopefully be confined to the throttle cable itself.
However, if the +5V feed is not present with with just the throttle disconnected, but it returns when the main harness is unplugged, there will be a short somewhere inside the main harness, but there may also be a short in the throttle cable as well.

You should be able to use a multimeter to check for continuity
(or very low resistance) between all of the pin combinations
(especially the +5V pins and Ground pins) on both the main harness and the throttle cable while they are both completely unplugged.
If either or both cables are shorted, it/they will need to be repaired or replaced.

I suspect the high current produced during the initial short caused by the LED failure will have overheated the Battery
+, Lighting feed and the Battery
- (Ground) wires causing the wire core to melt through the insulation on one of these wires and also melting through the insulation of one of the adjacent wires
(probably the Battery - has melted into the +5V) which has caused your problem.
Hopefully it will just be the throttle cable that is damaged. Check out
this post and
this post for further information on checking the throttle.
Alan