What's the best way to do CIF Withdraw/turn in/inventory ?

It's always best to do your own layout with your hand receipt.

Purchase what you failed to maintain accountability of, or ask for a statement of charges.
Learn from this inexpensive lesson.
You didn't turn in everything you drew if you're missing any items.

You should always do a personal inventory of your gear against your hand receipt before any type of turn in; or after any exercise that you had your stuff out on.
I'm confused on this part "rather than having to do the entire Platoon Layout". Are you thinking that doing your own layout will exempt you from a PLT level layout; or are you thinking that PFC Juarez somehow has the chutzpa to call a PLT layout to find your missing gear? The answer to the former is no, doing your own inventory doesn't preempt you from your PL or PSG's layout. For the latter , you'd be better served asking your buddies if anyone came up with extra shoulder pads and could you have them as your short two, than insinuating that someone swiped yours.
My two cents is to go to a surplus store / pawn shop and buy two serviceable shoulder pads and be done with it.