Onan 5.5 HGJAB won't stop!

Hello all,
New to RV'ing. I'm retiring in about a month and recently purchased a used class A. A Georgie boy 33' Velocity. Onan 5.5 HGJAB onboard. The previous owner stated everything works! Right.
Now to my problem. The day I looked it over she had the generator running and powering the front AC unit. So far so good. A few days after I got it home I decided to run  the generator. A very hot Florida afternoon. A few minutes after startup I noticed a minor fuel leak at the metal inline gas filter leading into the carb. Not wanting a fire I pressed the remote stop with  no result. I went to the switch located on the unit and still it would not shut off. Now I'm sort of concerned and after repeated attempts to get it to stop, finally pulled a wire on the fuel pump and after a minute or so it's off.
To make a long story short I wanted to make sure I could stop this thing the next time I started it. Wired a toggle switch inline with the fuel solenoid on the bottom of the carb bowl. Now no matter what, I can shut off fuel to the engine. This works. Also fixed my fuel leak by  the way.
Now I can run the unit just  fine but still the rocker switches will not shut it off. Neither the remote or the onboard although both work fine to start it.
I tried to query the fault code. After shutting it down with my improvised switch, I get 3 flashes indicating a service fault according to the manual. When I try pressing stop again to get  the 2 digit code, I get nothing but it continues flashing 3 times.
I've looked all over the internet for anyone with a similar problem but all I get is sets that have starting or running problems. Not stopping problems.
Anyone?

The fact that you can't get the fault code out either implies that the stop switches are not making contact or the wire between the switches and the generator wiring is open.  Most Onan's have a wiring schematic under the cover to the control box(at least the ones I have worked on). It could be as simple as a wire falling off a connection. 

Sounds like the ground wire from the module to ground is off. Another thing you could do is pull the fuse on the front of the generator, it will shut down then.

Two really good replies. Thanks brothers. I will let you know what I find. I really expected someone to say it was the control board. Now I have new hope that it could be a simple fix.