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Well the Apple Pro is a pretty forgiving chip design, but yeah if the install is really messy and you have wires running over other chips on the mobo the mod chip might actually be bleeding signals into other chips that it shouldn’t be, thus making that god awful squeaking noise you are hearing on the TV. Believe me I know that noise well. I once had a messiah pro that did that and it is not a good noise. It was easily fixed by rerouting the clk wire. I'm surprised your having that problem with the apple pro though, as the apple pro has its own on board clock (no clk wire) and most of the frequencies it produces are self contained.
As for it not recognizing media, are you getting the DRE screen with all media or just back-up media. It might be a laser issue as you probably know the V4 and earlier PS2's have crappy lasers.
But I for sure would clean up the install first and run the wires nice and flat on the modo before I was to test any thing else.
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