My first question is about the components used.
What is the master cylinder diameter?
What are the caliper piston diameters?
There are some kits available that have mismatched master cylinders. I know SSBC was one of the big culprits there, as well as some others who used the Corvette style masters.
I've never heard a groan from the hydraulic system on brakes. Boosters can leak vacuum and make noise and of course the friction materials do it, too. Is it possible you're hearing a problem with the bottom of the brake booster diaphragm?