And just what doest the BUTCH engine entail?
Some class skills hinge on non-class-requisite Primes. The best example is the Thief's ability to Find Traps which relies on Wisdom. A Cleric with Wisdom as a Prime will roll 1d20 + 6 (Prime) + Wisdom modifier, compared to the Thief without Wisdom as a Prime (1d20 + Wisdom modifier + level). Assuming the same Wisdom score, the Thief will take 6 levels (more likely 7 to 9 with a Cleric's very likely Wisdom 13+) to outperform the Cleric.
Ditch the idea of Prime Attributes.
Ditch challenges levels. I use the D&D 3.0e DC table.
Resolve everything with 1d20 + ability score modifier + level. Everything. Saving throws, stealth, anything that calls for a roll.
If it's relevant to your character class, you get +5. So the Cleric gets +5 to identify a relic, the Ranger gets a +5 to find his way in the wilderness, your Thief gets a +5 to do all thiefy stuff.
If you're using Secondary Skills (which I sometimes do), +5 is good too. Your gemcutter Dwarf Thief rolls 1d20 + Int mod + level +5 to appraise a piece of jewelry, and your bowyer/fletcher Half-Elf Ranger can roll 1d20 + Int mod + level + 5 to craft his own arrows.