You've had several great suggestions. I use NI B4 (the older version) software. I'm using an eMu Xboard 49 into my notebook computer to control it. I have that on my upper rack of the stand, with my Kurzweil 2000VP synth on the lower rack. I can use the 16 knobs on the eMu by assigning them to control the drawbars, I can use MIDI channel 1,2,or 3 to switch the keyboard to upper, lower, or pedal. I can also change the lower manual to some other MIDI channel and control it with the MIDI of the Kurzweil.
NI stopped making the hardware drawbar MIDI controllers, probably didn't sell enough of them to re-design for the new Europe required ROHS (lead-free) construction.) They still show up on EBay from time to time.
Pedals is a bit more of a problem. There are some 25 note MIDI pedalboards, but they are big bucks. Fortunately in my case, I don't play in our praise band trying to totally sound like a B3, I usually use the Kurz for bass sounds, and comp chords on the eMu for the Hammond sound.
I have another Kurzweil that has their KB3 emulator module in it, it gives me a keyboard that has enough sliders for all 9 drawbars. I carry it occasionally, but leave the eMu and older Kurzweil at the church so I don't have to set up a ton of stuff several times a week. The Native Instruments has a good sound that cuts through the mix well, although the octaves are considerably uneven (they may have fixed that in the II version, I'm not sure).
Jim