Well, after a day of testing, rewriting, reading and learning many things, I think I've finally got it all nutted out.
Checking my bits box, it seems I'd gone on a buying spree many years ago. I found an Uno R2, an Uno clone R3 plus, two Wemos D1 R1, and an Wemos D1 R2 board, as well as other 8266 mini boards but they didn't have headers on, so I ignored them.
I started from scratch on a sketch to just use a dummy while loop checking micros() for elapsed time for the pulse and the cycle length, and then ran every board against my makeshift oscilloscope. Here's a picture of one of the final results
So the Wemos boards are outputting 3.35 - 3.48ish volts. None of them has a smooth floor, with them all showing around 0.12 - 0.16v when set low. I'm not sure if the oscilloscope is picking these values up as a signal, but as you can see in the picture, this snapshot showed a frequency of 59.1hz, and I saw occassional peaks into the 70's, but most of the time it hovered around 49.7 - 50.2 Hz. The Uno boards when running the same sketch returned a very solid 50Hz, with only 0.1 fluctuation either side, but at a (very steady) 5 volt level. Given the Wemos are supposed to run at clock speeds of 80Mhz, I'd have thought they would have given a more stable signal. I guess this probably reflects the better architecture and design of the Uno boards.
So with a voltage and frequency (and I guess pulse width, as the PCScope software doesn't show a value for that unfortunately) about where my current receiver is transmitting, I hooked all the parts up to see how the KoPilot reacted to my introduced signal.
The result, in a word, was SUCCESS! I had the KoPilot mode switching from the receiver as normal, then pulled the signal wire which it was not in nornal mode. The KoPilot retains the current mode when it loses signal. I'll have to change this in the failsafe settings as I normally want it to go into return-to-home mode, but it was fine for testing. I then plugged the signal from my WeMos generator into the input of the KoPilot and (according to the mode lights on the unit at least), it went into manual mode, which is what I wanted. Plugging the receiver signals back in, in changed to the mode the transmitter was in when I left it.
Just to be sure, I changed the pulse width to try with 1000us and 2000us outputs from the WeMos, and the KoPilot lights changes as expected.
So, after all that, it seems I won't need the logic level shifter after all, but thanks very much to everyone for the help and insight. I've learned a lot and know what to do in future if I do need one.