When you enter into speed programming, it will program the speed for whichever rapidfire mode you were on last. So for example when you power up the controller for the first time it's on rapidfire mode 1 (whether or not you have rapidfire enabled). If you hold down the mod switch and hold down the fire weapon button, Player 4 LED will blink as you move to mode 2... mode 3... etc. So whichever mode you were in last, is the mode you will be programming the speed for, if you choose to program in a custom speed.
I'm thinking like the higher modes like 7, 8, 9 and 10 would be good to play around with for custom speed programming since I'm thinking those aren't really already set up for any game in particular.