While a ground wire is possible, there is only one ground wire that has to be removed to change the an MTX - the ground wire to one of the front bellhousing bolts. Unless you removed the upper intake, the only other one I can think of is the grounding strap from the upper plenum to the firewall.
Two alternator malfunctions can cause flickering lights.
The most common is a faulty voltage regulator. While you had the alternator tested, its possible that the problem becomes noticeable when the electrical system is under a load.
A less common alternator problem is a bad diode. These control the flow of electricity from the alternator, that has the effect of producing DC power from the alternator's AC output. Think of them as a kind of one-way valve that only lets the electricity flow in one direction (DC current).
When a diode fails, it allows reverse current flow in one of the three phases of the alternator output. The end result is that you have stable current flow through 240° of the 360° of each turn of the alternator, but at some point there is a minor reverse current flow during the 60° of the 120° of the bad diode's circuit.
That temporary reverse current flow is what produces the temporary dimming of the lights and lighted displays, that you notice as flickering. It is most noticeable at low rpm, and indistinguishable at high rpm.
If the alternator was tested on the vehicle, most of the simple testers don't tell you if one or more diodes have failed within the alternators rectifier bridge.
If the flickering is tied to rpm, take the alternator off and have it tested on a machine that checks the diodes.
