If I recall correctly:
TryCount_Item is the bonus roll count for having shiny charm.
TryCount_Research100 is the bonus roll count for having level 10 research for that species.
TryCount_ResearchPerfect is the bonus roll count for having a perfect dex entry for that species.
Do the math yourself as to what overall rate you want, and edit appropriately. Make sure you have the in-game bonuses active.
"Masuda method" is just breeding 2 things with different language IDs.
Since your photo has two different languages, yes, it'll gain the extra shiny rolls.
https://bulbapedia.bulbagarden.net/wiki/Masuda_method
Not sure which .NET Framework you have set up; be sure you're on at least .NET 4.6.1 (4.8 would work too).
PKHeX is gradually shifting away from the .NET Framework and will eventually jump to .NET 6+ (before or after November), which will no longer work with Wine.
Battle Version: When can you set the battle version in game? Are there any restrictions on doing so?
Moves: How would it learn the move? If it's something that is kept track of, does it have that keep-track value set?
Per the program's readme, you need to dump the full game as well as all patches into the romfs. Having unpatched (1.0) data will fail to be recognized.
dst are save states; save in game to properly get save files
"bak" files are backup... the program is likely overwriting the dst as you told it to, but it additionally creates a backup since you overwrote the original.
Thanks, will be fixed in future releases.
If you have the automatic backup setting enabled, you don't have to manually create them. Don't overwrite existing backups with that button, hence the (current) error
Without knowing what moves you gave it, can't know for sure. Ensure that PKHeX said it is legal.
Starting in P:LA, the game bad-eggs anything with a move it cannot learn.