Can anyone point me in the right direction for a virtual instrument that emulates that great slightly distorted sound Jon got out of his Hammond?

i thought it was hugely distorted!!!
 
LOL
 
just play a good B3 synth and route it into a modeled marshall plexi head, tone cabinet impulses, voila!~
 

I doubt you will find a canned sample of the Lord sound, however, you could have decent results building your own.   Lord used a Hammond C-3 through a Marshall Amp.   Maybe a Leslie in there as well.   Start with a good Hammond organ sound, add some overdrive, amp simulator and a rotary cabinet and you should be able to dial something decent in.  Here is a discussion below on this topic at the NI Forums.  
 
https://www.native-instruments.com/forum/threads/john-lord-ish-sound-for-highway-star.127523/
 
Jon Lord Equipment List.
http://www.thehighwaystar.com/rosas/faq/equip/lord.htm
 
Looks like you have some nice Hammond Organ samples to start with based on your sig.   Good luck.
 
 
Regards

On some tracks he used a RMI Electra Piano built in and layerd with Hammond. Add the distortion and this creates some of the unique tones.

I have used Native Instruments Vintage Organs (DI setting) and Hollow Sun's RMI layered in Kontakt and then put through Amplitube.

GSI's VB3 does a good imitation of the more conventional Hammond + distorted Leslie sound. Bitflipper had an excellent cover of Lazy using the VB3.

Strangely enuff, Synthmaster has an interesting B3 preset that allows a world of tweaking.

VB3 is awesome at emulating the distorted B3 sound, and let's you choose from different Leslie cabinets too.

VB3  +1

VB3 wins!

I'd also recommend VB3, although you might want to try some other amp sims with it. Lord's unique sound was obtained by running his (modified) Hammond through a Marshall head into a Leslie cabinet.
Although VB3's distortion feature does a good job of emulating a Leslie amp, it's not quite the same as what you get from a guitar amp.
 
He did have the organ modified so that he could play an RMI EP from the organ keyboard, which nowadays wouldn't require a soldering iron, just a MIDI cable. If you want to duplicate the effect of Jon's RMI, there are decent Kontakt libraries and you can use VB3's effects (they come as a separate plugin) to dirty it up.

Same company that makes Mr. Ray! I don't know how I overlooked this....sounds great, might pick it up, even though I'm happy with NI's Vintage Organs.  Wonder how it compares to the B-5 that I also liked when I heard the demos.
Might even pick up Mr. Ray, had it as a freebie many years ago, somehow it disappeared from my system after a HD crash, I think.