That's weird. I've got my Civil War Russian one and it's LOUD. Unity at 12 o clock or even before that. Which values did you change?
http://www.kitrae.net/music/big_muff_guts.html - have you seen that?
Baiscally, experiment with values of emitter resistors. Smaller value = more gain, try Q4 first. Also you can change collector resistor at Q4.
Besides that it Base-Collector resistors at Q1, 2 an 3 that influence gain. But I would first play around with volume recovery stage at Q4 to see what happens.
Maybe there;'s something wrong with tone stack? Try to bypass that and see what's the change in volume. Normally there is some volume loss there but that should be remedied by Q4 stage.