I know, from my own experience, that, since the bridge was shaved and the saddle lowered, the tone and volume must have suffered, even though you say it is fine now. A new, higher, bridge and saddle should greatly improve the volume and projection of an already great guitar. You're lucky to have really good luthiers available to you. Do it!

I had the plastic, adjustable bridge, on my vintage J-50, replaced with solid ebony and a bone saddle, and the tone and sustain improved by an order of magnitude. I was astounded.