Just to close this out, I thought I should post an update. I took Steve's advice and called Trace. He made suggestions as to what might be causing the problem, which I relayed to my engineer buddy who was then able to fix my amp. There were a couple components (resistors, I believe) that became disconnected. He re-soldered them and now the amp sounds great. The components more than likely came loose in shipment. The amp sounds really good and is very usable now.
Someone in a previous post questioned me asking Voodoo to "return the amp to stock". What I meant was that I wanted them to reverse the "mods" the original owner had done before implementing the "Jose HG" mod, I.E. I wanted a JCM800 with the Jose HG mod, not a JCM800 with Jose HG mod AND the mods the previous owner did. This was explained to Trace before I sent him the amp and, apparently, he did what he was asked to do. In the end, Trace gave me what I asked for.
Again, I meant no disrespect to Trace or Voodoo. There is nothing convenient or easy about using guitar and amp techs that are 5,000 miles away from your location. That's my problem, not Trace's. Thanks for all the responses.