Been working on the subjet this weekend. Got it compiling and seems that the serial works great.
Had to get rid of the timer interrupts, add new functions and new I/O pins. Couldn't find a way to use direct port manipulation on this board, but measured the digitalWrite function and it takes 120ns.
A couple of interrupts turn on the MOSFETs when the set current is reached, then a specific routine is used at 20kHz (that's common chopping frecuency, will try higher on the future) and turn them ON. Although the MOSFET drivers I was going to use had 500ns deadband, seems to not be enough so I added a small delay when they had to switch directions.