What is the best sounding Pre/Pro 7.1 channel with analog bypass.

Parasound P7.

No need for Y adapters. Its' a very good 2 channel preamp that has an extra 5.1. :)

It is much better constructed and sounding than the P5.

Hey Erik, he needs HDMI input/outputs.  Otherwise, I may have included P7.  But then again, he's asking for the "absolute best pass-through HT Processor".

What is your priority between stereo and HT?  What's your budget?  What sound characteristics are most important to you?  What speakers are you using?  Right now, IMO you're just organizing deck chairs on the Titanic.  Take a step back and let us know the answers to the important questions above and you'll get much better and more effective recommendations here. 

I looking to spend about $500 or less for a used pre/pro. So from $700 to $1000 new. Seeking clarity and imaging in the sound quality. Used mainly for HT, but want great sound for stereo. Using Chane bookshelf speakers with an Elac powered subwoofer in a 12'X12' room.  

My first reaction is to tell you to save up until you can get something better and not to expect great sound quality from a $500 pre-pro (or even much higher ones for that matter).

Having said that, Every time a new pre-pro comes out the manufacturer claims big increases in sound quality, when really it's mostly new features (room correction, video handling, atmos, etc.) and pre-pros tend to lose their value faster than most audio gear so you can find some bargains on some decent gear if you don't have to have the latest and greatest. 

In your price range for used, I'd try to pick up an Onkyo Integra DTC-9.8.  I'm not sure if it has all the features you want, and I'm not sure why you want to run the Oppo directly to your amp.  The pre-pro has balanced inputs and 7.1 analog inputs.  You can set it up so that you're using the DACs in the Oppo if that's what you're after.  There are a lot of reviews about this unit and a few of them for sale under your budget.