Well, I'm afraid that I don't have any answers for you. An ogre is CR 2 but has 4 HD and an ECL of +6. An unclassed ogre PC has superior ability scores and the equipment of a 6th level PC, compared to the MM ogre that has hide armor, a greatclub, and a spear. The PC ogre is definitely more dangerous, but is it CR 6 dangerous? I would guess it closer to CR 4, but I would need to see it in action to be sure. Perhaps you could start from the basis that CR does equal character level (monster HD + class levels) for monster PCs, then modify it upwards if the monster possesses truly special abilities (like mind blast at will). Unfortunately I think that you're in mostly uncharted waters here, since most people have no need to determine the CR of their PCs.