Carwarr wrote:Great news! I am glad that I started this whole thread!
So am I, as it has given me an incentive to find out why the Mega 2560 would not work through its USB port 

 .
I had ordered a Arduino Mega 2560 and have been waiting for it to come from China before you started all your work with the Nano.
I will probably try to get it to work with the Mega, but if not, I will just buy a Nano Every.
I am glad about that, too, as I now have someone else who can test my fixes for the Mega 2560 so please try to get it working with it. You should certainly be able to do so and I am happy to help if needed.
To use the Mega 2560 through its USB port, without a JP1.2/3 cable, you will need RMIR v2.13.5 which I shall shortly post in the 
RMIR Development folder.  In that version the Options > Advanced menu will have an option "Find all Arduino".  You need to select that option.  It is persistent, in that once set it will remain set in all instances of RMIR until you deselect it, so you only have to do this once.  It also takes effect immediately, so you don't have to close and re-open RMIR before using it with a JP1 remote.  The only other difference from the instructions I gave for the Nano is that pin 4 of the remote's 6-pin connector goes to SDA and pin 6 to SCL on the Mega 2560 rather than to A4 and A5, as A4 and A5 are dual function pins on the Nano but separate single-function pins on the Mega.  If, like me, you use Dupont patch cables and have a Mega board with sockets rather than pins then you will need male-to-female ones for those connections.
I hope you will try it connected in this way, but if you also have a JP1.2/3 cable then you can use the Mega 2560 as a JP1 EEPROM adapter with the current RMIR version, or if using v2.13.5 then with or without the "Find all Arduino" option selected.  The connections for the JP1.2/3 cable are its pin 3 to Arduino GND (the Mega has 3 GND pins and only 2 are used by the connections to the remote), its pin 4 to Arduino RX0 (which may just be labelled RX) and its pin 6 to TX0 (or just TX).  Just those three connections, but you need to have both the Arduino USB cable and the JP1.2/3 cable plugged in to USB ports, the Arduino one to power the board and the JP1.2/3 one to send the signals.  I suggest setting Remote > Interface of the RMIR menu to JP1.X Serial and selecting the port as that of the JP1.2/3 cable to avoid any confusion or spurious signals being sent to the Arduino.
Do please let me know when the Mega 2560 arrives and how you get on with it.