The ecu is back, and in one piece.....thats hard to complain about, no matter the price.
Regarding the Pair Valve.....You dont exactly need to remove it, now, or forever. I ended up removing mine when I added a power commander as I already had the plastic off, and the tank removed.
For you, right now, your bike does not need plugs, or the power commander. If you want to avoid digging into your bike, all you really need to do is stop the air from entering the valve.
My bike is a California emissions equipped bike, and yours is newer, so it might be different. I had two hoses to block. Both were accessible from the inside of the airbox.
I dont think this picture is of a ninja 1000 pair valve, but they are all so similar, it does not matter.
If you block the open hose, that wont let air into the system. That hose connects to the bottom of the airbox. I think people used marbles, 3/8 bolts...pretty much anything to stop the air flow into it, and it works just fine.