When I record the Hammond audio it is full and deep sounding.  When I play it with a midi track it sounds tinny.  Is this some sort of midi echo?  I've tried unsuccessfully to resolve this but haven't found the answer yet.  Thanks for your help

My first thought was turning off local echo - or you will produce sound both with keys and through midi via Sonar.
 
So next idea is that pan audio full left - right or the created stereo image might start cancelling out each other.
 
So maybe both - that two unison keys sounds fuller - but when just one midi sound thinner and tinny.
 
I envie you that organ - I was very close getting one when there were an add some month ago.
Now I have a Korg CX-3 which isn't bad though.

A MIDI feedback loop would be my first guess, too. What you need to do is disable "Local Control" on the synth during playback. 
 
I have an XK-1, which I assume is similar. There are two MIDI setups (which they call "templates") available via the MIDI setup menu: "Seq. Record" and "Seq. Play", which is their roundabout way of saying "Local Control On" and "Local Control Off".