That was unfortunately a typo - or at least should have been updated as they went into production
It should read 0,1,2,5 (default) or 0,1,3,4 - why 1,3,4,5 isn't an option I can't completely recall, but I believe it was that we had to choose between USB or I2C without having 8 jumpers (since they wouldn't fit). When we release the next version we'll be taking a careful look at USB vs I2C usage and which is preferred or if there is a way to accommodate both.
I apologize for any issues that causes with your project.
Schematic:
https://s3.amazonaws.com/digistump-resources/files/6348a83c_motor.pdfYou could cut both jumpers to p2 and p3 and the jumper from one of them to p5. Then connect p0 to p3 and I think that would work. With the solder jumper to p5 cut and p4 bridged.
PWMA would then be p3
PWMB p1
DIR A p5
DIR B p4
The solder jumper pads should be easy to connect a jumper too
And if the motor is the top board you could solder a jumper right to the p0 pin and just cut the leg off that goes into the shield below it so that it is left unconnected to the rest