J-440, since you said your M/C has 2 different size port threads that means you have the Mopar type M/C with the plastic reservoir and not the all metal version. The primary or front brake line needs to go to the rear port and the rear brake line goes to the front. The reason for this is that there is built in volume proportioning- the front brakes get more volume of fluid.
The newer type all metal Wilwood M/C is different- port sizes are matching and the front port is for the front brakes.
I'd recommend to add a factory type metering valve/distribution block for 3 reasons. Hold off , a warning light and the safety of closing down 1/2 of the system in the event of a hydraulic failure. There is several different options for doing this, including some new trick aftermarket pieces.
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