That is actually one of my older EQ configs. I've since made an improved version of it which tries to not dull the treble too much like what you mention. You may want to try that, it's somewhere in this thread.
+100 for Equalizer APO. Awesome program and a must imo for the HE-400. I wouldn't only want to tame the treble in music players, but games and Youtube videos as well. I don't use the program anymore since moving on from the HE-400 but I'd strongly recommend the program to anyone. I'll have to take a look at that GUI app you posted, looks really helpful. I was editing the config file before to create my EQs which was a pain in the neck!
Sounds good, although I think I will still need a portable amp in the future, but it's good to know that for now I will still get good sound straight from the iPod.
Still haven't made my mind up on a good portable amp though.