66 barracuda - converted to dual master cly, could stock pushrod be too short?

Manual brake MC's usually come with a push-rod & dust-boot. Most likely your new MC was intended for power brakes. But, that probably doesn't explain it. More likely, the later dual reservoir MC has a deeper rod hole in the piston. Having to adjust the brake switch is a given. As long as the MC bottoms out before the pedal hits the floor (test it dry), that is all you need. I put an MC from a 95-99 Breeze on my 64 Valiant as a manual MC, and the pedal wound up in about the same place, even w/ a 2-4 bolt adapter plate moving the MC fwd slightly (photos in my post). I was just lucky.