Don't know the Roland controller, so can't give you specific details how to program it.
Yes, you can program the Factors by MIDI in the way that you want.
Basically you set each Factor to be a specific midi channel number … Say ModFactor ch 1 and PitchFactor Ch 2.
Then get your controller to send a program change on Ch 1 to change to the patch you want on the ModFactor and send the program change on ch2 for your PitchFactor.
The exact program change number is worked out as 1:1= 001 1:2=002 2:1=003 2:2=004 3:1=005 etc