Hi, changing banks only switches the 404's own pads to play the new bank - not external midi when every midi note plays a particular sample no matter what bank you select on the 404.
Download the 404 manual and you'll see the midi note assignments are fixed one note per sample "pad" spread over 2 midi channels. So to access each bank of samples you either change octave on the pedalboard and/or switch midi channel to get the second set of 404 banks.
However - you'll have your work cut out using the 404 as an instrument sampler - it has no envelope shaper - so sustained tones like organ will be set to loop which will have to be trimmed just so to loop naturally (especially if vibrato/rotary is in the sound). That said, your style may suit shorter organ stabs so you won't need to loop them and the lack of envelope shaper is no loss with organ (or mellotron). Short sounds would have to played long enough to include the natural decay or cut off prematurely when you release the pedal key, although you can set each sample to play to the end even after the midi note has sent note off. ~A bit of reverb/echo will help hide the sudden endings though

Jim