I'm not sure if tow holes would affect the manifold. In my 04. 5 diesel I had one hole with no long term affects. I had a full set of gauges (a total of four)and a monster exhaust (cat back) system. For years I never had a programmer . I had been to the dealer a number of times and nothing was ever said to me. I would check with the dealer to see if it would be a problem. But with these new trucks they can tell iff you have ever installed a programmer so that shouldn't be an issue. But you'd be more likely to void the manifold warranty if it should develope a crack. You could also use a product like the edge insight (gauge only) that monitors: Barometric Pressure, Battery Voltage, Boost, Calculated Load, Corrected Speed, DPF Pressure, Engine Coolant Temp, Engine Speed, Fuel Level, Fuel Rail Pressure, Gear with TCL, Intake Air Temp, Mileage Coach, MPG Instant, MPG Average, Post DOC EGT, Post DPF EGT, Post Nox EGT, Regeneration Status, Throttle Position, Time 0-60, Time 1/4 mile, Trans Temp, Vehicle Speed.