@sleepvertical so your save from the cartridge is working. Hence why it's loading on PKHeX.
However to load it into the 3DS VC, a few things need to happen:
1) The save needs to be named specifically sav.dat
2) Extra bytes at the end needs to be added.
If you provide the save, I can do it for you.
As for Stadium moves, they shouldn't be there, but it's not like the game would freeze up cause they're there.