So just to complete this discussion...I redid my brakes completely.
-Old, non drilled rotor (I don't think this made a big effect, I'll put back the cross drilled when I get a chance.
-Brake pads were not plumb, I ground them even. I think this may have had a big effect.
-The biggest improvement was a direct, new braided line from MC to Caliper. The feel on the lever is much better now but the best part is how easy to bleed the system is. Just tug the line this way and that to release the bubbles. I did all the bleeding from the MC.
-The MC had an integral brake switch so I just jump wired the brake lights to that, getting rid of the over engineered junction block.
The brakes feel much better but still not nearly what my other bikes feel like but I think what it is is what it is until I'm ready to pony up for a complete system upgrade to modern brakes from a later bike.