I have a simple question, does the transmission effect the engine controls? When my car shifts into 4th gear at any speed sometimes the engine cuts out for a split second. The check engine light does flash at the same time. Then it runs fine,never does it in any other gear.

 

Not completely sure what you're asking; but I think the answer would be, both yes and no. The TCC is controlled by the ECM, and there's a switch in the trans that tells the ECM that it's in 3rd or 4th gear; which are the only gears that the TCC is supposed to be activated in.

Stumble on shifting sounds to me like a tuning problem; specifically a lean condition at that moment.

Years ago, before there were even electronically-controlled carbs, there were certain carbs (Hitachi) that had a "vacuum accelerator pump" for this exact reason. The idea being, that if the driver was holding the throttle at a constant opening when the trans shifted, there would be a sudden increase in the load on the engine, which would cause the carb's main circuit (jets/rods & venturis) to go to a richer state, but no corresponding accelerator pump shot to cover up the time lag that it took for the fuel flow to rise to the necessary level. The "vacuum accel pump" was added to give a little shot of fuel at that critical moment, triggered by the sudden vacuum drop from the shift. The same function exists in the ECM. Your tuner can control it.

 

That makes sense to me. At wide open throttle I don't seem to see it.
thanks