It's because for the 7M, Toyota numbered the coils based on the cylinder they fire (1 and 6 is C1, 2 and 5 is C2, 3 and 4 is C3), so the firing order is c1, c2, c3, c1, c2, c3 etc.
For the 2JZ-GE DH-61 equipped cars, the coils are numbered from front to back in the valley between valve covers, (2 and 5 is C1, 3 and 4 is C2, 1 and 6 is C3) as the coils sit on cylinders 2, 4 and 6 and have wires running to the odd cylinders. so your firing order is c3, c1, c2, c3, c1, c2 etc.
So you need to convert the coil numbering from the 7M-GTE to 2JZ-GE formats. To do this you use:
output 1 = coil 3
output 2 = coil 1
output 3 = coil 2
Bottom line is that C1 from the DH61 should go to the coil firing cylinders 1/6, C2 should go to 2/5 and C3 should go to 3/4