So, I think instead of doing one big cumbersome project, I'm going to do it in steps.
1. Add an expression pedal jack, carrier in/out jacks, and a square wave switch.
I just wanted to make sure with you how you do the square switch, I think you wire a 15k resistor from pin 9 of the wave generator and also run pin 9 and pin 2 to a selector switch to select square/sine right?
Problem: I have an old keyboard volume pedal that I used to use as an expression pedal for my now destroyed johnson analog delay. I was thinking about rewiring it to work with the frequency analyzer (it is actually wired to ground the signal I believe

The pot in there is twice the resistance of the shift pot (which is 250k). I think the best solution to that would be to add a 500k resistor in parallel with it to make it closer to the range of the 250k shift pot. Am I right to think that, or am I overlooking something?
2. Add a sequencer in jack and build an external 8 step sequencer (3 is a little too much now that I think about it!) The box would have several stompswitches- one that bypasses the original pot and switches to the sequencer, one that switches from step to auto, and one switch that steps through.
Problem here is I have to make 4 connections from the sequencer to the frequency analyzer, so I'll probably use some other kind of connector besides audio cable (so I can keep it to one cable going inbetween these two boxes) If I wired the 2pdt that changes from the shift to the sequencer into the frequency analyzer, I could do it with a stereo cable, but I don't want to mess up the layout of my frequency analyzer with big ugly stompswitches. Messing the sides up with tons of jacks and little switches does not bother me though.
Any suggestions of the kind of cable to connect the two?
3. Add an LFO to modulate the pitch of the VCO. I'm not exactly sure how to do this or which LFO schem to use here. Or if I can even use an LFO since technically it is not CV that is controlling the VCO. I could always make a vibrato with a square/sine switch on it, and put it between the carrier out and carrier in.
4. Add more synth module type stuff. I'm thinking a sample and hold sort of thing would be cool, but I am not sure if I quite understand how sample and hold works. I read the Moog control processor manual (I don't own one, but it is nice for the ideas) and it didn't really explain it very well.
Well I'll explain how I think it works and then you can correct me hopefully.
It has two inputs, one for LFO, one for the signal getting modified, and the output. Everytime the LFO rises above 0V, the S+H samples the signal getting modified, and holds the output at where that signal currently was, until the LFO passes by again.