I cannot test the physical board right now but I can think through the problems I was having.

This is the relevant part of the circuit that drives the RUN light in the original schematic. 

And this is how it looks in my schematic:

Christopher at randomvariations describes it as follows with the abbreviated familiarity of an experienced engineer:

"The final chip, a 7402 (quad NOR,) inverts the SYNC line, driving an RC network to stretch it, before it is finally buffered to drive the run LED. "

If I have understood correctly, the SYNC output pin of the 6502 pulses each time an op-code is fetched. SYNC is therefore low when the 6502 is not running and low between pulses. The 7402 inverts the lows (as 1B is tied low so the NOR becomes effectively a NOT) so that the LED is driven high (via the 7417 buffer). The capacitor slowly charges while SYNC is low / IC1 pin 1Y is high and the stored charge smoothes over the instants when SYNC is high /  IC1 pin 1Y low so the LED should be lit continuously.

The fact that the LED is not lit suggests that either this part of the circuit is wrong and/or that the SYNC signal is always high. This should be my next point of investigation.