First: Try out a bunch of different 'tweaks' with the game. It does sound more like an issue with the emulator than the ROM itself... Could even be something with the ROM that the PC Emulator can simply overlook. Either way... don't put away that Robe and Wizard Hat yet. It may still turn into a beautiful woman.
Second: Not likely. The ISOs would want to gain access to the HDD and that would not happen. Also, I don't think Linux would install properly onto a non-SONY HDD. Could be wrong about that, though.
Last: I use HDLDumb and HDLDump. You run a small server program on the PS2, and use the app on your PC to send an ISO over the network to your PS2. There's even a GUI that'll do it that makes things pretty painless. Just make sure you use the same version for both programs. If you try to use 0.8.5 on the PS2 and 0.8.6 on the PC, it'll crash. No lasting damage, just annoyance.
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