No, a smaller bore will produce more pressure but move less fluid, so you have to push the pedal farther.
Part of your problem may be that the brakes were designed to run on a boosted system. If the caliper piston bores are small, then you'll need more pressure to make them work. Depending on the brake system design, you may need 1,000-2,000psi. Mechanical systems typically run in the region of 1,000-1,200psi under operation. If you have a system that needs upwards of 1,500-2,000psi to work, you'll probably need a booster.
If you have plenty of room for additional pedal travel, you could try dropping down to a 7/8" bore m/c.
Who cares how much horsepower it has, all that matters is how fast it goes!
Untested 331, lots of suspension, chewing up corners.