So if i do a
digitalWrite(5,HIGH);
digitalWrite(5,LOW);
(5 being the new BLANK Pin i want to use)
after the line of code which does the 4096 GSCLK pulses, this should give me the same result?
Yes.
I just need to find the line of code that does the 4096 GSCLK pulses then? is that done in one of the libraries?
There isn't one, it's being done by a hardware timer (Timer 1).
Then i should just grey out the line of code that does the original blank Pulse?
Ditto.
(...that's why you can't move it, and why you need to do it in software instead!)