First of, I'm really sorry for the frustration and the waste of your time. I really wasn't aware of all the problems that might occur and I didn't fully understand the condition of your bike. Actually, this is why I always discourage people to post me their PGM unit if they are unsure about their bike.
My suggestion is to place the PgmIV unit aside and inspect all of the other electronic components that plugs to your wiring loom.
As you said, after the repair the rc valves still didn't work and new problems constantly keep coming through. Obviously, something is changing in the meanwhile and it's not the Pgm unit I reckon.
From what you are mentioning, you are trying to connect the battery while somehow the PGM unit is engaged aswell.
The PGM unit triggers at least three electronic relays that supply power to the rest of the wiring loom, so there is a lot of current there and sparks may occur, especially if there is a loose joint. This is not an issue of your bike, this is the norm...
As I've mentioned to you, the Pgm unit was lacking the on/ off switch that engages when the card is inserted.
Have you now fitted it to the unit?
If I remember correct, you do not have an LCD display aswell.
Do you still have the "Function" switch on the panel?
I described to you how a reg/ rec is and where you can find it.
Were you able to locate it and measure it?
If you still believe that the PGM unit is the only wrong thing with your bike, I can make you a drawing template to check that all the grounding points are correct and you do not have voltage running the earth points.
Just say so and give me a couple more hours...
By the way, I still believe that buying a second PgmIV unit right now is a really bad choice.
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