Thanks for the response duhvoodooman. When I first read that thread, I thought what was happening may have been common for the pedal and I was wasting everybody's time, but I learned a little more tonight.
I performed mod #1 as described in the thread. I didn't have a 68k resistor so I used a 51k (closest value I had). This did not reduce the overall distortion when the knob was at noon, but it did considerably clean up the dry signal when the mix is turned all the way clockwise. As described in the thread, it's almost transparent now when I have mix all the way to the right.
I then performed mod #2 (2.7k resistor) and verified this brought my vref up to 4.7. After adjusting the trimpot again I tested. This did not noticeably affect the sound when compared to results at the previous step. I decided to not go further with the mods for now since the others seemed a bit more permanent.
As a final step, I put a good opamp and tested after each in IC1, IC3, IC4, and IC5 (remember I had already replaced IC2, and with the dry signal sounding good I figured that was okay). At each step I continued to have a relatively harsh, distorted sound, only getting worse as I turn the mix knob counter-clockwise.
EDIT: I see IC1 is actually responsible for the dry. I knew this before but had a late-night brain poop. So I suppose the issue could also be in the LFO/bias section. I have a signal probe and could dig deeper, but getting the time for that kind of involved work is a challenge for me right now!
Other than playing with the mix knob I've left my controls like this:
Depth: about at noon (occasionally turning it up when biasing)
Rate: 2 o'clock
Mix: variable
Res: all the way counter-clockwise
Stages: 4
At this point it seems like it's in the phase stages portion of the circuit (I have been testing with 4 stages), possibly a transistor that is clipping. Although I can understand the circuit at a higher level, it gets a little out of my wheelhouse when getting to the transistor bias, etc (I've just recently built my first fuzz). I have checked my solder joints several times and am at a loss. I wasn't planning on building another phaser for a while, so I'd still like to figure it out. At the very least, I've learned quite a bit about this pedal in the process!
EDIT2: This is my first time really trying to understand a circuit such as this. Where does the control/bias network in the bottom center of the schematic connect in to the phase stages? I can't determine the output of that network. I guess I need to brush up on my schematic reading skills as well.
Thanks for your help everybody!
John