I am concerned with the CR calculations of monsters and their associated difficulty levels.
In AD&D, the monster XP Values were often messed up, but since it took 50 creatures on average to level up, it wasn't much of an issue. But in 3e, the CR system was WAY wonky. I think that the most accurate system I've found was the "Immortal's Handbook Epic Bestiary" appendix titled "Challenging Challenge Ratings". But I don't think it's the be-all-end-all of CR calculators.
However, I really think that the only way to calculate the CR of a creature is to first see what the "average" character's stats are at every given level, so you have something to compare the CR to. The only way I can see this being done is to create a database of PCs of all races, classes and levels (including templated characters like half-fey and phrenic), made by newbies, average players, and powergamers. Make sure it includes all the character sheet stats and average damage by round for at least one tactic.
A note about templates: The level adjustment would have to be recalculated too, then the whole set recalculated with the new LA. Template CR adjustment must be calculated by comparing each stat adjustment with the discrete derivative (wrt level) of the stats of non-templated characters, not the stats themselves. If the derivative is nonlinear, then the template CR adjustment must be as well.
Once the database is complete and the averages/deviations are calculated, all you have to do is compare your monster's appropriate stats to the PCs and see what level it would be. This would also reveal weaknesses and strengths of the monsters and classes.
Also take into consideration "I win" spells and spell effects (for example a spell weaver can cast 6 magic missile spells in one round at one target, inflicting 30d4+30 hp with no save and no attack roll unless a shield spell is active. Then there's always the problem of flying invisible 5th level PCs dropping glitterdust and ranged attacks on earthbound CR 21 creatures with no ranged attacks. I'm not even going to go into the scry-and-die tactic). Many of these problem spells are already taken care of in the beta, but I bet there are still some to consider.
On a side note, please don't use monster names like "blacktoe merauder" or "iceblight basilisk". Those kinds of names just sound juvenile to me (I admit it's just a game, but you have to admit that "Cthulu" has a much more ominous ring to it than "Squidhead Devastator").