More info is needed:
Does your CDI look like this:
(This is a 5 pin CDI as compared to a 4 pin CDI).
If so, then what is the wire color on the Kill Switch pin in your wiring harness?
Normally when you disconnect the remote control module the only thing that changes is that you can no longer turn off the quad with the ignition switch - you have to use the handlebar kill switch insted. But you say that doesn't work. so there are more issues here to resolve.
There are aftermarket remote modules out there. Does this remote module look like a factory installation or does it look like it was added later?