So, a few weeks later and with a friend who had successfully rooted his phone, we tried one last time to fix it. For some reason, the tablet decided to boot into a Honeycomb (3.2) A501 ROM (without us doing much to it), so clearly something took, possibly from a few weeks back (not sure why it chose not to work then, but whatever).
So, I followed steps to downgrade to 3.0.1 and root, then ran blackthund3r's APX flasher to reinstall Clockwork Mod, which also took nicely. Then I carefully followed the steps to install the Evil Alex ROM (and made sure I downloaded the actual ROM this time and not the patch). Again, this all went fine, until I rebooted. At this point, it got to the ANDROID logo screen, but got stuck there. After about 10-15 minutes, I decided to reboot again - same behaviour. So I went back in to CWM, followed the steps above to perform all wipes, format system 3 times, then format flexrom again, reinstall the ROM. Now it gets stuck on the Skrilax_CZ's bootloader screen with "Booting primary kernel image" screen. I can still happily get into CWM, but I'm at a loss what else to try.
The only difference in what I did between the first install of the ROM (where it got to the ANDROID logo screen but no further) and the second was to remove the SD card after installing the ROM (before rebooting). Well, apart from also formatting system 3 times as mentioned above. I'm assuming removing the SD card or not shouldn't make a difference since the ROM should be installed by that point anyway.