If you're getting P3401 for Cyl-1 then I'm guessing the other MDS codes are P3425 (Cyl-4), P3441 (Cyl-6) and P3449 (Cyl-7).
P0013 is set when the PCM detects that the actual voltage of the Variable Cam Timing (VCT) Solenoid Control circuit does not match the intended state.
P0016 is set when the PCM detects that the deviation between the camshaft position and the crankshaft position has exceeded the maximum acceptable value.
What P0013 has in common with the MDS codes is that they share the same ground circuit. The VCT solenoid is located under the intake manifold in front of the MDS solenoids (attached to the VCT phaser assembly)
P0016 may be getting set because of P0013.
Check the wiring harness/connectors and ground connections.
VCT electrical connector (1)
VCT solenoid (3)
.