I just finished my overtone special mini build and I want to reach out and make sure everything is working as it should.  As far as I can tell, the controls are all operating properly but I have a couple of concerns.

When neither button on the footswitch is on, the amp really doesn't get loud like I would expect.  I'm an apartment player at the moment and would describe the amp as loud when the master and volume knobs are at max.  Is that normal?  Then, when I hit either button on the footswitch it gets loud as all hell!  Additionally, the green button on the footswitch makes the amp super bright and loud.  I'm not sure what controls alter that tone or volume.  I guess I'm worried that the clean channel is supposed to be louder.

Let's start here and see what we can work out.

A good first step would be to post an inside chassis circuit board view of your amp, a picture is sure worth a thousand words, especially here.

If you're not getting ample volume, when neither the Overdrive or Boost foot switch is engaged, something is definitely up. A 20w amp isn't going to get crazy headroom, but it should have a substantial amount of dB's, just under as much as any other high wattage design.

I have almost the exact same issue. The clean channel doesn't get as loud as it should and is much more affected by the boost than the OD. Were you able to find a solution?
Edit: Lowering the gain to cleanish settings balances the Preamp boost. You can also decrease the overall amount of boost by increasing you Bass Treble and Middle controls and decreasing Master to compensate.