Another Hauptwerk user asked me in a private message to provide a bit more detail about the wiring I did. Since it took quite a lot of head scratching to figure it out, I thought I would help.
Setup - The original wiring harness had too much damage to it, and since HWCE2 (the board I used for the conversion) uses ribbon cables, I found it the easiest to cut all of the wires at the switch. This left a stub of wire that I then removed with a soldering iron and flux. I bought a desoldering iron, but I found that most of the contacts didn’t lend themselves to being desoldered that way - flux when used properly was way more useful. The original circuits have a number of capacitors, resistors and other elements that could be useful, but I just threw the whole lot in my local electronics recycle bin, along with the amplifier and power supply. Perhaps someone else may want to recycle and reuse those, or find someone else to use them. Once the console was gutted, I took advantage of the opportunity to clean the inside and outside of the console with soap and water, being careful to avoid the switches.
Manual wiring - The HWCE2 kit from MidiBoutique has an 8x2 matrix input. I also got the bundle with the SM8x8 spread boards. These boards take care of the need to add diodes to each matrix switch, which saves a lot of time and effort. The spread boards themselves have a 5x2 contact set for each set of 8 keys (8 switches and 2 returns). The Yamaha Electone divides the keys into boxes of 6 or 7 keys, each having between 4 and 7 switches per key with a common return rail for each set of switches. The challenge provided by this is that the SM8x8 spread boards only want one return for each 8 keys. I tried initially wiring a common return for all of the spread boards, but I think the voltage differential was too much, and the boards had too much trouble picking up the switch activations. What I did then was to use two layers of switches, so that each set of 8 keys had only one return. This is tricky, because it meant I had to wire each set of 8 on two different layers of switches, starting with the second box. To make the soldering easier, I found that I could take out all the switch boxes, then wire them all together, then transfer the boxes back to the manuals together. Tricky, but it worked out. I prepared the spread board end of the ribbon cable with the included connectors, gently tapping in the plastic top with a hammer, then cut the other end of the ribbon cable with a hobby knife to the right length, splitting each wire according to the appropriate length, and stripping the ends as I did that. I could then solder each wire to the appropriate contact. To attach the circuit boards to the wooden base, I drilled four holes per board, and attached them with metal standoffs and small hex bolts on each side. I attached the boards prior to cutting the ribbon cables, so I would have the right length in the end.
Pedal wiring - The pedal wiring was the most straight forward, as each switch was isolated, and I could wire them in sets of 8 easily. The tricky part however was soldering the switches in place, as they are very firmly attached to the bottom of the organ. I wired them into two groups so I could use the styrofoam coverings to keep the switches clean, and so the ribbon cable would come out from the left edges of the styrofoam covers. I wired the ribbon cable to a board close to the single hole in the wooden base of the manuals.
Stop tab wiring - The most complex switches were the stop tab switches at the top of my organ. These had multiple stop points, representing the different intensities of each organ stop. To wire these, I desoldered all of the resistors from the switch, then used a multimeter to find which combination of contacts represented the bottom most stop of each switch. I then soldered the ribbon cable to the appropriate positions on the multi-switch. My model also had a “rhythm section,” which is a complex switch set that turns off previous selections when a new one is selected. I wanted to use that for combinations. I also used a multimeter to find out which contacts to use, but I also found that if there were multiple channels to a return circuit, then the switch wouldn’t work. What I did was to use a hobby knife to destroy the extra channels to the return, and then the switches worked as desired.
Future directions - I still haven’t wired the expression pedal. The plan though is to connect the light bulb in the pedal to a variable resistor, then that to a 24 v transformer. That will power the light, which will let me get resistance readings from the optical resistor. A friend of mine has said he will help me figure out how to wire an operational amplifier and resistors to the circuit to get the right gain range for HWCE2 to receive a linear output from the sensor as I move the expression pedal. I have seen other, more simpler sounding wiring schemes on other forum posts but honestly I don’t understand them - so I’m going to go with what my friend can help me with. I’m not sure I’m going to wire the knee pedal - I’m quite tall and it’s in an awkward position for me to use.

Here is a closeup of the wiring for a set of 13 keys. On the bottom are the contacts use to connect for each key. You'll see here for each key there are 8 contacts (though only one is used per key) On the top is the return rail wiring. The last two wires on the ribbon cable are soldered together, then to the contact for the first return rail for the first seven keys. For key number 8, the key contact is soldered to a different contact on the bottom, then the blue wire you see on top is connected from the first return rail on the left side to the second return rail on the right side. Then, this starts over for key number 9. Of note, I had to remove the resistors (hidden on this picture under the switch box) from the circuits that I was going to use, then re-wire them with ordinary wires.
Hopefully this helps!