OK. Looks like the game still freezes from time to time (every 30 mins - more or less), when it crashed I turned DS off and on - and I can play again. It's not freezing for forever, only randomly. I don't know if repacking done anything, but you can try it.
Download "dslazy", open the app, find yor rom and open it in the app, press "nds unpack" and then "nds packer". It will repack the rom file. Save repacked rom where ya want and copy it to your card.
You can also try changing text files from EU version to working JAP version - but it didn't work for me. Filenames in both roms are the same, but filesizes aren't, maybe AP is checking filesizes somehow.