As pointed out before, the wire that you thought was going to the wait is actually going under the wait and into the DIO function. This wire is meant to signal the DIO to configure the port and then write to the port when i=0, and to just write (no configure) when i is not zero. There is no need to configure each time through the loop, the first time is enough. It is considered bad wiring to route a wire under another function.
As far as choosing lines, I like to start with DIO0(pin 25). I would choose DIO0 for CLOCK, simply because it is easy to change the first bit (LSB) for every clock cycle you want to send. You can choose any other comination you would like. Perhaps DIO1 for STEP, DIO2 for DIRECTION, and DIO3 for PRESET. I normally choose the line that is most likely to change as the lower bit and then go up from there. Just write down your choices. You would send 0000 for clock low, then 0001 for clock hi. To combine clock with others you could send something like 0010 for step with clock lo, then 0011 for step with clock hi. To change direction send 0110 then 0111. I am not familiar with your stepper motor so I just using these values as an example. When sending the values, it would be easier to display the value in binary (set show radix visible), then you could see which bits are high/low and you would know what functions they correspond to (clock, step, etc). You could also use a variable for the data with clock low, then just add 1 to the variable for data with the clock hi. For instance, you could define StepForward=6 (b0110) and StepBack=2 (b0010). Then to step forward you would send the variable StepForward to the DIO, then StepForward + 1 (b0111) for the clock. That way you don't have to mess with the values each time you want to send a command. Since the values are constant, it is OK to use local variables here. I hope this is clear to you.