I FOUND SOME SPARE TIME.
I wired up the Uno with all the other components and it worked fine apart from the not fully printing the "off to the loop" message.
I then started looking for another way to provide the IR led with its 38khz signal. I found a gem here.
https://forum.arduino.cc/t/how-to-create-a-38-khz-pulse-with-arduino-using-timer-or-pwm/100217/12
This is it:-
const byte LED = 11; // Timer 2 "A" output: OC2A
void setup() {
pinMode (LED, OUTPUT);
// set up Timer 2
TCCR2A = _BV (COM2A0) | _BV(WGM21); // CTC, toggle OC2A on Compare Match
TCCR2B = _BV (CS20); // No prescaler
OCR2A = 209; // compare A register value (210 * clock speed)
// = 13.125 nS , so frequency is 1 / (2 * 13.125) = 38095
} // end of setup
void loop() { }
It produced a nice 19khz signal. (my mini runs at 8mhz, I suspect this is why). These few lines of code mean nothing to me but I tried experimenting with that number "209" and eventually found that if changed to 104, it gives me what I want. I looked at it on a scope and it looks the right shape and everything!
Now all my code runs properly and I have loaded it onto my Green box prototype.
All is well.
How quickly I become happy when things start working again.
Big thanks to you guys for your help. (and Nick Gammon)
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I did run my IR led through a transistor back along, but I did some tests changing its inline resistor, I think over a range of 15 to 115ohms and found no real advantage anywhere so I opted to use a 100 ohm resistor which means that the led only draws 20mA. I thought this should be well within the pins capabilities so I decided to remove the transistor. I have run it for 5 days continuously since then and it seems to work ok.
It also seems fine without extra modulation of the signal.
Next I am going to try and fit my system with some NRF24L01 units. Watch this space .