It seems that there is quite a bit if tubing between the check-valve and each individual nozzle/intake runner. That leaves a good bit of water to be ingested, even though you've got a check-valve in there. I'd recommend placing the check-valve as close to the nozzles as possible, with the ideal situation being a check-valve for each nozzle placed just before it. I'd guess that a good bit of the water that's present in the lines just after the check-valve is getting sucked in to the engine, and then when the W/I system does kick on it's got to purge all that air out before water is finally injected.
The vacuum present in the intake manifold is MUCH higher that that which is in the intercooler piping before the throttle body. It's no wonder you didn't have problems like this with the old setup.
BTW, is that a 6G72 in your GTO? The engine bays of our USDM 3000GTs/Stealths are mighty cramped with that engine in there. I can't imagine how it must be with that GTO!
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