Spongy pedal after big bolt pattern conversion

I'm having a problem with a spongy pedal after doing a big bolt pattern conversion. I have to pump the pedal once or twice to get a decent pedal and even then, the car doesn't stop like it did before the conversion. Here's the specs before and after the conversion.

Before:
Kelsey Hayes front disks, re-sleeved with stainless sleeves a new stainless pistons done by Stainless Steel brakes about 20 years ago. Stock Raybestos pads.
10 x 1 3/4 rear drums - stock with Raybestos shoes
Aluminum Master cylinder (don't know what bore size)
Wilwood proportioning valve

After:
11 3/4 Cordoba rotors with 1997 Viper calipers mounted on AR Engineering adapters in the front with locally made stainless braided brake hoses, Hawk HPS street pads
10 x 2 1/2 rear brakes from a mid 80's Diplomat - stock everything, new Raybestos parts
Same Master Cylinder & Wilwood prop valve as above

Bled the new system thoroughly, ran about 1 1/2 quarts through it.

Used the same brand silicone brake fluid on both setups. The original stuff stopped good, had a firm pedal. The new stuff just isn't the same. I have to pump a time or two to get a firm pedal and then it stops OK, but not as good as the old stuff. It should stop way better, given the increase in swept area.

Looking for ideas as to what to do next to cure it and/or troubleshoot it.

The only thing I can think of is doing another bench bleed of the m/c.

Here's a before and after picture, just to make it more interesting. FYI - both calipers are rear-mounted, I only have an old pic of the right side and the new pic is of the left.