Wilwood Disc Brake Issue

Could be they just need to be bedded in.

But I suspect the biggest issue is you lost a fair amount of piston area with the new calipers. Depending on which caliper you had (2.6" piston or 2.75" piston) you lost either 10% or 23%. You didn't say what size rotor you had either so hard to say how the 12.19" rotors changed the leverage.

Best guess is you got used to a big piston caliper and lost a fair amount of piston area so you need to apply a fair amount more leg pressure to get back to where you were. A smaller bore MC would help that.