An MSD system should not share any of the vehicles OEM harnesses. I make my own dedicated MSD harness that shares nothing with the original wiring and mount the box under the back seat which is much cooler than the motor compartment. If you want to access the box, just lift the seat up-no tools needed. Clean and never any problems. This is an example of a car I did that has the hidden componentry.

Yes, the coil is an MSD coil ...The radio suppressor is just for show.

MB