I don't know why the ISOs you're building don't work, but here's how you can run the decompiled game in recent development versions of Dolphin:
First, make sure that the game has been extracted using either wit or a version of Dolphin that's recent enough that it doesn't have the DVD Root and Apploader settings. (If you've extracted it using some other program or an older version of Dolphin, it likely lacks some important data.) Then, once you've made your changes to the game and want to run it, just ask Dolphin to run the sys/main.dol file.
First, make sure that the game has been extracted using either wit or a version of Dolphin that's recent enough that it doesn't have the DVD Root and Apploader settings. (If you've extracted it using some other program or an older version of Dolphin, it likely lacks some important data.) Then, once you've made your changes to the game and want to run it, just ask Dolphin to run the sys/main.dol file.