is there a way to disable the starting it in neutral function? its weird because sometimes i can start it in gear while holding the clutch and other times it wont start unless its in neutral.

 

those "sometimes it will start" are you also holding the front brake handle?
My rubicon will start without having it in N if I hold the brake handle.

 

i never thought about that, ill try it once i get it back from the shop.

 

There is a switch in the clutch perch. It has 2 wires going to it. If you cut those 2 wires and connect them together, the safety switch will be by passed.

 

instead of cutting them and ruining it in case you ever want to change it back to stock, just connect them to an automotive type fuse. You may need to file the blades on the fuse to narrow them a bit, but you are essentially doing the same as connecting them together, but without cutting the factory connectors off.