I'm not a number cruncher by nature, though I do understand your equations. Creating them, well...
I'll try to help where I can, based on my last four years of experience with my monk.
First off, at least level 51+ (and I suspect the vast majority of dmg equations on monkly-business is *for* this area), monks are on an entirely different damage table from all the other classes. Most of the damage tables on mb were created so that monks could figure out their tables, so I suspect this is why your equations, designed for that level/skilllevel, don't jive.
I am not entire sure you can eschew level completely from the equation. I believe you will need to end making two equations to be accurate, one for 50 and below, the other for 51-65, and include a check for level. I know the monk's damage changes based on level there, and *not* skill.
Another thing to consider in your equations, and this may be affecting some of your error, is duel wielding. Primary and secondary weapons do not get the same damage output. There is a primary hand bonus to all weapons. The secondary weapons, however, either do not have a damage bonues applied or have a miniscule one. Try structuring the equations with this to model damage, and see if that doesn't yield a more accurate result.
I've created a spreadsheet to keep some data. As a middle-level raiding guild, I see a fair amount of action against mobs like SoRZ, CT, Tormax, ToV, etc. I'm going to keep tabs on min/max damage given and received, and keep tabs on the AC and ATK at the time (as possible... the last part may prove more difficult to do then say).
Grummet