here is the deal.
Your original system the coil had 2 wires running to the + positive side of the coil. (yellow & brown resistor wire)
Yellow wire ran from the "I" on the starter solenoid to the + side off the coil.
Brown wire is your resistor wire from ignition switch to + side of coil.
(You said you have already replaced this wire) that is correct.
Both those wires, One from the starter and one from the ignition switch needs to be connected to the MSD box. The Red wire on the MSD box.
The one from the starter (yellow) supplies power while the engine is turning over "START MODE" then when you release the start mode on the key it goes to the ignition power from the switch.
Al