Ugh, what a bummer! I have a 6600 and it's a good and hardworking machine. I would be really furious if I was having that much trouble with an 8900, I know that's not a cheap machine at all. Unless you're confusing sheet metal with fabric I can't imagine how it's your fault this is happening.
I THINK you can take your machine to any Janome dealer and have warranty work done, it doesn't have to be through the person you bought it from. Is there another dealer you can call or take it to?