Write HALF the cycle time to MR3 and MST3
Set bits 10 and 27 in MCR to make it reset and reload.
Set bits 10 and 11 of EMR to make it toggle on match (that’s why you need half the cycle time)
Set bit 0 of TCR to make it go.
then set bits 0 and 24 in TCTRL5 in the A/D to make it trigger from input 5 and run command 1.
if you need an interrupt when it has finished, set bit 21 of IE
in the A/D, set bits 0 and 24 of TCTRL5 to enable the trigger from input 5 and run CMD0 ( or whatever command you want it to run)
if you want an interrupt when it has completed the conversion, set bit 21 of IE.