Do you mean the pushrod that connects the brake pedal to the master cylinder (or booster) is a different size? If the length is wrong, you might be trying to use the wrong hole in the pedal swing arm (upper hole is for manual brakes & lower hole is for power brakes).
Flyer, the 4th gen brake push rods don't use an adjustable clevis like the earlier years. They have a ring formed onto the end of the pushrod that attaches to the brake pedal swing arm with a pin. One of my parts books lists a different pin for manual vs. power brakes. I'm not sure what the difference is, but this might be Ron's problem if the pins are different diameters or lengths.
Also, 4th gens use a large bolt for the upper pedal hanger pivot. The bolt is longer on the manual trans setup to accomodate the clutch pedal.
I remember having some issues with the length of my brake rod, also - when converting from auto to 4-speed. I thought the issue came from my car having power brakes and the parts i got the clutch/brake pedal assembly from being manual brakes. Anyway, when performing these mod's etc. there is always a certain amount of "fabricating" necessary to make eveything work properly. My solution was to use a a threaded sleeve with nuts on both ends and modify two push rods to get the proper length and have plenty of adjustment. Worked great and gives you a certain sense of satisfaction when you fab and utilize these special custom parts. A little ingenuity goes a long way when restoring these Nova's.
When I converted mine, I found the pin for the brake push rod was closer to the piviot bolt hold than on the arm for the automatic. I drove the brake rod pin out. I measured the distance on the automatic pedal. Drilled the proper size hole in the 4spd arm in this same location. Drove the pin in this new hole. Everything works fine. I hope this helps.