Hi,
I eventually figured this out. According to the ReadMe.txt with the extender it says to use:
Extinstall 3A79ext-notes.hex yourirfile.ir newirfile.ir -sig=$0600
I didn't know what yourfile.ir and newirfile.ir were and was beavering away at this. Eventually I found out that yourirfile.ir is the unextended ir file for the remote and that newirfile.ir is the output file from Extinstall which is the extended ir file for yourfile.ir. This is very hard for a newbie to figure out; I thought extinstall would actually flash (install) the extender onto the remote. From what I can tell ExtInstall only convert an unextended .ir file to an extended .ir file.
I also found out that I needed to copy the files into the IR803 directory (extender .hex and .rdf, unextended .rdf, extinstall.exe). Then I did a factory reset on the remote (hold Setup, 9-8-1), copied the remote to base.ir (in IR803 directory) and then ran:
cd IR803
extinstall 3A79ext-notes.hex base.ir base-extended.ir -sig=$0600
Then to install the extended base-extended.ir file onto the remote I used IR (or RMIR) to flash the remote. I had to press through the warning that the signature was different (this is expected when switching between unextended and extended .ir file).
Now instead of using base.ir as a starting point I used my configured .ir file (except I removed the macros because they would be recursive with an extender) and then I did:
extinstall 3A79ext-notes.hex config.ir config-extended.ir -sig=$0600
Then I flashed the remote with config-extended.ir.
In the ReadMe.txt is says to not flash an extended enabled remote with an unextended .ir file. To do this you should first disable the extender (hold Setup, 4 blinks). What wasn't clear was if you can flash an extended remote with the extender enabled with an extended .ir file. Flashing an extended remote with an extender .ir file with the extender enabled (or disabled) seems to work fine.
Hopefully this helps someone.