Despite what the build notes say should I run a series resistor at the output of the doubler *AND* a parallel one, which i have already, at the amp input?
No.
This would be correct impedance matching, but you have to take the voltage division of the two 50-ohm resistors into consideration, so you'd only have half the voltage for the 74F74, which is not enough to trigger it correctly. I think the original designed forgot this, which explains the footnote.
On top of that, driving a 74F74 directly from a coax input is bad design.
My suggestions would be:
1: use a standard CMOS 4046 and power it from +8 V (78L08). This will give you around 6 Vpp at the bipolar output.
2: use a series resistor at the sending end and the parallel resistor at the receiving end. This will give you 3 Vpp for 74F74 with optimum impedance matching.
3: use transient protection at the input to the 74F74 combined with a buffer/Schmitt-trigger (on edit: badly phrased, should be: protection -> buffer -> 74F74). The bipolar output will not go sufficiently low to trigger the 74F74 correctly.