So there's nothing obvious, but my dad went ahead and replaced the FET on the bass pickup channel on the preamp card since it's a possible cause of the problem if it's intermittent it oculd test fine here and work fine for you until it doesn't.  
 
We'll send the card back to you today and you can tell me the results once you reinstall.

Thanks Mica!  I'll let you know when I get the card and reinstall it.
 
Todd.

Would Mr Sony repair your dvd/camera/tv etc.
Having the BOSS repair your gear is priceless!

This is why I love this organization in more ways than one.

Mica, your dad has great insight!!
 
I received the card today in the mail. The neck pickup appears to be working for me. At first I was horrified by the amount of distortion, but realized that the gain had been turned all the way up on the PF-6 card. This sounds great on my Fender Twin Reverb, but not so good on my practice amp. I guess it just doesn't have enough headroom.
 
After adjusting the knob down about halfway it sounds great through both the practice amp and the Twin Reverb. Man, this is a great guitar.
 
Thanks again Mica, and tell your dad thanks as well.
 
Also thanks again to Sam for selling this guitar to me (I hope you are not too sad)
 
Man, this is a great guitar.
Todd.

I had just about had my wife talked into the electronics upgrade and a refinish if I were to have had to send the guitar there to be fixed.
 
Todd.

Congrats Todd!!!