To repeat somewhat...
The problem is that real organs do not have sustain pedals. So, some Organ plugins do not sustain the sound when CC64 (sustain pedal) is received.
One easy workaround is to not use those plugins. If you open an organ sample in a standard sample player plugin, most likely it will recognize CC64, and sustain the sound as you want it to, without any need for CC # modification. Easy.
Having said that, I would never want the sustain pedal to sustain my organs. I make the sustain pedal select the speed of the Leslie effect. (fast/slow)
Usually, most organ programs assign the Mod Wheel (CC1) to that. So, if you swap CC64 to CC1, the sustain pedal will control the speed of the Leslie.
Or, you can use other CC numbers. For example, CC65 turns on Portamento. (acts like a mono lead-synth if your keyboard supports that).
More important, you might want to swap CC7 (volume) to CC11 (expression). So your expression pedal actually controls expression (swell), not volume.
(Some keyboards might send expression pedal as CC11 correctly. My Studiologic controllers do not. They send CC7.)