I got mine to work, finally. Basically by trial and error and redoing EVERYTHING, multiple times. I did all the work on my actual Windows 10 computer, using Notepad+++ (which fyi, the older cue files I did on my Mac did NOT have any weird characters on them). Formatting the memory card (switched cards as well), downloading new files, trying different versions rips (v1.1 or 1.0 or 1.3 or whatever until one worked), got it in order somehow.
Had a bunch of fun trying to get
PSIO's Systems Console software to actually merge games which had multiple bin files - that was a fun 3-4 hours...basically just keep restarting the program until it actually works - and make sure to move the files to the C: drive (they did NOT like my 260mb/sec external SSD).
Also had a bunch of known-working (on RP3, Retroarch on PC and Mac, and on my Sony PSP and Vita) images give me "High Fragmentation" errors (on a freshly formatted memory card, AND on a second brand spanking new SD card). Again, just downloaded different versions until one worked - seems to be no rhyme or reason I can figure out.
Also kept having the system reset and had to redo the initial setup a good 8-9 times - mostly after a game froze on the menu.
So all in all, to get 86 games prepped for the PSIO, it probably took me a good 12 hours or so over a couple nights. Now that I know what's involved better it would probably take me only a couple hours, but still a pain. I was seriously questioning if I did a part of the internal mod incorrectly to have all these problems since that was the hardest mod I've done to date (just SO TINY parts to solder to, and super small traces to cut I couldn't even really see through a magnifying glass even).
On the positive side though, I haven't experienced any sound being messed up like people have mentioned (and I'm using an ancient, but nice, Bose Acoustimass stereo system). I think games are running a bit faster too - I played through about 20 minutes of the inverted castle in Castlevania SoTN and didn't notice the type of massive slow-down that usually has when I'm running it on a regular disc (could have been the part of the castle I was in though - couldn't find an area with like ~10 monsters on-screen at once which is when it usually gets unbearably slow).
Question: I did find a small handful of games where I had to change the EXTDSP Mode from the default K1V3, to off, to get a game to load. Is there a way to save this setting so I don't have to do it every time? I named the end of the file so I remember to do this upon launching, but was wondering.
I also have to learn how to add multi-disc games together in the same folder with the MULTIDISC.LST properly (besides the FF's, think theres only maybe 2-3 from my collection which have multiple discs - currently just loaded up the first disc of those). And have to research how to add game art, and I think there was an option for a background image too maybe?