Have you tried new plugs at the same time as unplugging your control box?
CO settings would be a good place to start, and if you have an A/F gauge, let it cycle and ready itself before you start it, without the control box. I'm thinking you are too rich at idle, and it's simply fouling the plugs. Especially if you say it runs fine for a few minutes...
Make sure your plug gaps are set correctly for your application. Plug gaps are critical on most boosted stuff, especially when you start lowering compression. This can help fouling at idle somewhat.
Also (if you didn't already know) it's hard on the plugs if you don't let the engine get up to operating temp before you shut it off. Starting it multiple times for a few seconds or so will most likely leave the plugs "cold fouled" after a few times of doing this. Been there, learned that a long time ago the hard way...
Start with fresh plugs, no control box and afr gauge ready. You should be ok at idle or a few revs without the control box, but dont put any boost to it obviously (so no rips around the yard), and watch the gauge to see if it gets really rich before it dies.
If it does what I mentioned above, You'' have to start looking into the CO settings first, then fuel pressure regulator, possible stuck injector, etc, etc,