I've been running my clean cx3 kronos organs into TH3 with good result.  I like setting up parallel, maybe one side with a head only and one side with a cabinet.  You can make one side harsher and the other warmer then slide between them.  
 
I love the Jon Lord sound.

Great suggestions, thanks. Tbh, it hadn't dawned on me to combine a synth with a guitar amp. So, I just tried one of the Hammonds in Dimension Pro (the bottom one on the list, can't remember its name), and put it through an AC30 amp sim, which was a good starting place. I get the idea and will continue tweaking!

thepianist65
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.

The guy who wrote VB3 has been pursuing the perfect Hammond emulation for more than 20 years. Unlike many clones, it's not based on samples but rather on wavetable oscillators, so it generates tones the way a Hammond does, one harmonic at a time. He takes into account the subtlest elements, such as crosstalk and tiny imperfections in tone wheels that make the real thing not-quite sinusoidal.
 
Add one of the best Leslie simulations and MIDI-automation of every parameter and you've got the full Hammond solution - for fifty bucks (don't wait for a sale, it never goes on sale). With it you also get the effects portion (distortion + Leslie) as a separate plugin that can be used with guitars and voice. 
 
Real physical drawbars and bass pedals available, or you can go all out and get a Crumar Mojo that combines waterfall keys, drawbars, half-moon rotary switch and VB3 into a physical instrument that's as close to a B-3 as you're going to find.
 
The Mojo has been on my wishlist for a while, but until recently could only be ordered from Italy. Now it's carried by Sweetwater. Comes in dual- or single-manual versions, $2300 and $1500 respectively. If I didn't owe my insurance company so much money, I'd have one now. I'm salivating just thinking about it.

I found exactly this last week after installing Miroslav Phillamonic 2 and playing around. I'm away from home right now, but it was in the organs, drawbar, distorted, and I sat and played Child in Time for a good 15mins.....
 
I'm yet to really delve into MP2, but it's very tweakable. But I agree with what your already trying. That's what I would have done. Until now lol!!

Thanks, Dave, will have to look for this in MP2.