Clipping devices really don't affect the EQ, just the overall signal level.
Is there any chance you mixed up your 823 and 821 capacitors? Because that would cut a massive amount of lows in the "wet" overdrive signal. Or mixing up the 392 and 391 capacitors. That would cut a massive amount of highs from the wet signal. The combination of the two would result in a fairly narrow Q mid boost similar to a wah.
Midrange "boost" in overdrives is not a boost of the midrange, per se. It's not like an EQ with the mids turned up. It's a reduction of lows and highs, and then usually, a boost of what's left over.
So you can restore the lows and the highs, and flatten it out a bit. But the Klon also has a massive clean boost, so you may want to reign that in a bit as well so that it's not so noisy or prone to squealing or some sort of self-oscillation.
The 823 (.082uF or 82n) capacitor just to the left of the drive pot eyelets affects the low end. Using a larger value here will increase the bass. Something like a .22uF would probably give you a nice bit of low end back, but not too much.
Using a smaller value in place of the 391 (390pF) capacitor will return some of the high frequency. A 100pF would probably be good here.
The Klon has a wet/dry blend. After returning some of the lows and highs to the wet signal, you are going to increase the overall wet signal level, and thus throw this blend out of its original ratio. The 47k resistor is the pre-blend wet signal level resistor. Increasing the value of this resistor will reduce the wet signal level. You might not need to change this. Or you might not want to if you prefer it. But if you need to change it, this is where it would be done. I'd probably try a 56k or 68k.
_________________
*patience is a virtue*
Please do not PM me. email is prefered.
keith@buildyourownclone.com