Ok, so I did the direct to phono input vs into BBE pre-amp then into an AUX shootout which resulted in learning that the BBE was actually 3 db quieter than straight into the phono.
So I went back to the phono input and compared the CD input with the same album on CD vs on vinyl. I found that the CD was around 10 db louder than the vinyl.
I then got into settings and found that you can adjust the output of any individual output, as suggested in this thread. I used a db meter on my iPhone and balanced it out by pumping the phono output up.
For all I know, the CD output is hot. Once I get other devices like my Apple TV and Direct TV hooked up to it I'll have more reference and be able to decide if that needs to come down as opposed to balancing anything further to that.
So for now, crisis adverted.
I still feel like overall the system is a little crisp sounding. While in the settings I looked for how to look at the treble adjustment, but I couldn't find anything. The speakers are the same, so maybe the Sony I had was just a darker sounding receiver and I'm not used to hearing my tweeters so much. So maybe I'm just not used to it yet.
Thank you all again for your thoughts, ideas, and input. It's really helped an old dog learn some new tricks.