When shortening buttstocks, I've found several things to be very helpful.
I bought a checkering layout tool that has an adjustable, sharpened arm that rides along the top of the forearm, to give a matching border line for the checkering panel. It can also be very useful to mark the end of a buttstock when shortening, if I want to maintain the same angles as the original cut. After removing the pad, lay it on the end, and make a scribe line to match the amount you want to remove. If a fella don't have access to a table, chop, or band saw with a fence or guide, you can cut it short of the mark, and use files and a sanding board to trim the butt to the line. Not as important on a synthetic, but on a wood stock, the scribe line also helps to keep chipping and splitting down.
On the single synthetic stock that I shortened to 'youth' proportions, I ended up losing the "bosses" inside for the buttpad screws. I built the area up with epoxy, then drilled it for new screws.
Changing the dimensions of the pad after shortening the butt may reveal the reinforcing plate in a lot of the recoil pads, especially those made by Pachmayr. You may end up purchasing a new pad one size smaller to avoid that pitfall, unless you don't mind bare metal poking out the side. I've cut a LOT of pads down by clamping the buttstock to the bench top with the pad screwed down, and using one of the cheapie rubber sanding disc things made to be used in a drill. An angle grinder would be better, but for many years, my budget wouldn't even allow me to pay attention.... In any event, use a fairly coarse grit, 60 or 80, and keep the pad moving so you don't 'burn' the rubber. Also, use a couple of wraps of good masking tape, the blue stuff that comes off easily, and if you see that the sandpaper is marking it, time to back off.
Hope some of this stuff helps someone......
BTW, I'm one of those he-man types that screams like a little girl when a Hobo or Black Widow decides to make it's presence known on the bench. I find that the buttstock doesn't do nearly as much damage to 'stuff' sitting on the benchtop, like coffee cups and ashtrays, as the ball peen hammer I usually use.