Did you make sure to properly bleed the master before installing it? They're a PITA and usually need to be bench-bled, at least on the cars I've changed masters on (no DSMs, for the record).

Is your fluid level staying consistent when the system is sealed up and you're pressing the brake pedal? Does it still have the stock rubber brake lines? Did you inspect the caliper (boots)? Any slow leaks on any of the components?

The brake pedal will always feel stiffer with the car off because there's no vacuum, especially if you press it multiple times. It's supposed to be much easier to press with the car on.