I'm too much of a noob to answer if you are screwed or not.
I can tell you that I recently got the Trilogy working but only after updating Hermes IOS to v4 which just came out. http://www.wiihacks.com/wii-custom-s...os-v4-out.html
I wouldn't do the offline wad install since that crashed my wii but after running the installer from the homebrew channel and letting it do it's downloading thing everything went back to normal.
Follow the direction (easy way) here, http://www.wiihacks.com/software-bac...logy-work.html for installing and running the Trilogy.
One thing the tutorial did not mention is that you must choose IOS 222 to run the third game. The other two worked on 246 but I left the setting at 222 after running Fusion and they all work great.
I ran all three Metroids from both WiiFlow and USB Loader GX which I updated recently through it's own update in settings.