Precarious situation, AKA; thin Ice. The ”Controller” Your referring to is the the DFPC - Yes?
A DFPC controls your Fuel delivery and, if malfunctioning, needs to be replaced ASAP.
The CPU needs to be hooked up to a Scantool, verify it’s still able to communicate Data correctly, (Do this KOEO, initially) .
The fact your Pony’s running indicates you may have narrowly avoided disaster, Wouldn’t run it until you have replaced the DFPC.
Being it’s a 2017, and N.N.A., Contacting Roush in addition for some free guidance would likely be your most potent option to get you the right answers, get your Pony back on its Feet@1-800-59Roush. Good luck!