Hmmm...second person to give this warning. Maybe I am missing something.
I posted before your post came up explaining the custom strat pickguard. You'll be fine. (1 minute late if you look at the time stamp!)

As for the screw size to use, I think you'll be fine with #4's but the mounting hole in the pickguard for neck may be a factor for what fits best.

I have a similar guitar, but with 1 volume, 1 tone. I bought a strat pickguard blank and cut the holes myself.

Click image for larger version. 

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