Lowest common denominator dude... The amp didn't change. Your guitar did. Dramatically it sounds like. It's your new guitar's tone you don't like. One of the dangers of building customs... You just can't be sure what you'll end up with til it's done.
To get to the root of your tonal dilemma you'll need to isolate the variables that changed in your custom build. It sounds like the neck didn't change, so what's different with the body? Is the tone wood the same (I.e. was your old guitar basswood also)? Are your pickups the same? Body shape can change tone also, but I doubt going to a fireman shape would change your tone drastically.
In short, stop messing with your amp, which is the same amp you always liked before, and figure out what you did differently on your new guitar that you don't like. Pickups would be the first place I would start...