Finally got my remote working, and accepting upgrades. I think it got into some weird, buggy state because of the POWER/button search and 980 code resets. I had a few buttons not working at all, not even lighting the power button when pressed.
Fixed it by uploading the original .ir file and then the upgrade. Modified discrete HDMI 1-4 to the buttons right above the number pad. Digital/Analog, EXIT, Guide and i-Manual doesn't seem to have any functions on my TV, EXIT does work.
Manually learnt, Logitech Vol+/- and mute. Need CR2025 batteries for the A/C remote. Want to re-learn/verify the A/C codes again. The learnt signals for the Logitech speakers shows up fine and verifies with the existing upgrades.
Discrete HDMI input -> functions upgrade
A/C functions -> DVR buttons learning
Logitech speakers -> volume/mute buttons learning
Thanks The Robman for finishing the RDF. I think the remote working to mostly where I wanted. Slightly disappointed that macros don't work. To power on/off everything.
Main question... Is there a way to save/input/upload learnt codes using RMIR. It would be nice to program learnt codes and upload it, instead of manually learning.
This was the cheapest learning remote I could find, I had a hunch it was JP1 capable. At worst, I would just manually learn everything needed. I'm happy I can now pull/verify codes from other remotes. MrMoody mentioned the Onn 6-device remote also has learning, so I'll pick one of those up as backup.
This remote is almost identical to my original Sony TV remote. Now with the upgrades and learning, I have it functioning pretty much as I want controlling the TV, A/C, and speakers.

Original Sony TV remote on the left, Insignia Sony remote, RM-VL600, Charter OCAP 1060BC3.
Loved the RM-VL600 learning remote, 8 devices. Big Volume/Channel buttons. Clean/simple layout. Used it for 15+ years, but the buttons are dying. Opened it up a few times to clean it, but it's not working anymore. Manually learning/programming it is a pain.
Yeah the directional key pad is way too small and too close to the circular buttons. I also mistakenly hit the outer ring buttons sometimes. Also, the buttons seems a smaller than the original Sony remote.
Big thanks to everyone commenting and helping out!