Getting Strat scratchplates to fit can be a problem, even if you've done it a few times before. There is always a wire that moves, even though you are sure you've aligned everything perfectly.
Which particular ST kit is it? Most come with loaded scratchplates. And with the 22-fret neck kits. the scratchplate has to be fitted before the neck is screwed on.
From the photo, the pickups seem to be sitting quite low, but the screws should still be protruding more than anything else. I'd measure the cavity depth and the length of the pickup screws beneath the underside of the scratchplate, just in case the factory have fitted longer screws than normal.
It would also be helpful if you could post a picture of the underside of the scratchplate, just in case anyone can spot something out of the ordinary.
I've got a loaded scratchplate from a GST-1 handy that I can compare it with.
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