RiverRat - nice find. I had a 1955 M3 for a few years and eventually ended up selling it to pay for my tone tubbies in my guitar rig. If I may provide some comments -
A Hammond M3 is indeed a "baby B3". Unlike other designed-for home use Hammond console organs, the M3 series does indeed have the same tonewheel technology that drives thie B3, C3 and A100 - which by the way are identical with exception of the cabinet design - and the A100 has internal 12 inch speakers. It lacks something referred to as "foldback" that the B3 series has which, briefley, gives it some extra growl by using some of the signal from the upper octave keys to add back sound from the lower keys. It also has less keys on each keyboard, but still enough to play seriously on, no presets - which are the black keys on the far left side of the B3 series and fewer slidebars to adjust the intensity, or, in another perspective, the contributions of the 8 different tones that make up the sound.
What is does have is all tubes - and if your M3 has been ravaged and has crappy tubes - just buy some good ones and put them in. Probably a good idead to do to get it working. Also, the speaker is wired to have current going into it - and you need to watch because you can shock yourself even when not plugged in.
Not sure why you would want to convert it to a midi contoller other than perhaps you are looking for the real waterfall keys to get a good organ feel. Dude - either buy a Nord 3 that weighs like 17 lbs or do yourself right and get a leslie - even a 125 would do - with the correct hook up kit so you can get fast and slow speeds - and you will have the coolest sounding organ - way better than any midi generated organ - due to the tonewheel technology and more importantly the leslie. It's all about moving air around the room and nothing does it like a leslie - thats why they sound soooooo cool. Pretty hard to gig with unless you have a truck and a crew - but way cool for your house or studio.
I way regret giving up mine - but it took up a lot of space and I'm a guitar player - would love to get another one someday. Pics of my M3 are in photo section of my myspace page. Good luck and think about the potential before you chop it up.