from the intellicomm box in the 4th photo...there are 2 pairs of green and yellow wires. One pair runs into that RS-485 connector that plugs into the pump
The yellow/green pair from screws 11/12 on the Intellicomm are the digital speed comm cable to your Intelliflo pump.
and the other pair runs into the heater...(on the heater) the green wire runs straight to the ground there, the yellow wire coming out of the intellicomm box is wire nutted into the black/yellow wire inside the heater then runs up to the back of the pool heater thermostat and then there is a black/yellow wire that also jumps over out of that same wire nut to the "TH" terminal on the heater control.
That connects the heater to screws 9/10 Program 4 on the Intellicomm so the Intellicomm knows when the heater is running to change the pump speed.
On this junction box below is where the pump, heater, booster pump all tie in and run back up to their respective breakers in the aqua switch box/power center.
So there are four conduits going into the box but you don't tell me where each conduit runs to.
You talk about the respective CBs but have never shown a clear picture of the CBs in the Aquaswitch nor labeled what each CB powers.
On these 4 photos...from the intellicomm box in the 4th photo...the 2 blue wires are running from the intellicomm box over into the transformer and I cannot tell if those are the wires for the booster pump or the main (VSF) pump
The blue wires trigger 7/8 Program 3 speed on the Intellicomm.
but of the blue/red/black pairs in the intellicomm box...one of each pair runs to the relay for the heater, VSF main pump as well as the heater.
The red wires trigger 5/6 Program 2 on the Intellicomm.
Nothing is connected to 3/4 Program 1 on the Intellicomm.
The black wires connected to 1/2 on the Intellicomm power the box.
I suspect that the blue wires and red wires connect to the relays in this jumble of wires. You need to follow the wires and show exactly what screws each wire connects to.
The first photo is where the timers for the booster pump as well as the heater/pump ramp up connect to the relays. It is looking from the rear of the photo of the front of the aquaswith box where the 3 out of 4 slots are taken up and labeled as relays.
I see 3 relays in the picture above but you don't tell me which relay the heater, filter pump, or booster pump are connected to with which wires.
When you show me a snippet view like below I cannot orient what I am looking at with what the manual shows.
Please show me entire boards.
If this is still a bunch of gibberish, please let me know and I will start shutting off breakers and pulling wires completely out to hopefully make it more clear.
What are you looking to accomplish with this exercise?
What are your questions?