there's not really a way for you to guarantee the build for the buyer. they will just have to trust you to get the parts, build it and ship it to them. unless you own a business doing it and have some type of insurance that way, they won't have any fall back if you chose to keep the stuff for yourself. well other than taking you to small claims court.
all a complete trust transaction. this is what i think you are asking anyway. swapping id pics or something like that could be a way to get some assurance for the buyer. i've done this before as well for members and had no problems but then i wasn't planning on scamming anyone
as for shipping it together, pack the inside of the case with material to keep it all steady in shipment. packing peanuts or foam is a good way, though a tight packing with newspaper would also do the trick in a pinch. idea is to ensure the cooler and gpu don't flop around in transit. they should be as steady as can be tightly packed in there. having them flop around is a good way to snap the pcie slot or cpu socket or worse crack the mobo do to twisting forces. slots can break from just the weight of the gpu sagging as it sits on your desk. so pack that sucker as tight as can be to ship it. then make sure to insure it through the post office, ups or whatever. this way any damage they do can be recouped.
i repack the case assembled into the box it came in. they are pretty sturdy and already have all the foam to protect the case. then i pack all the manuals, extra pieces and so on into the mobo box. they are big and shaped well to hold all this stuff. then ship this separate so he has all that stuff. all those stickers, cd's, manuals, ties, extra screws, psu cables if it's modular and anything else they ship with the parts like extra mounting brackets for aftermarket coolers...... basically i give literally everything except the boxes everything came in. even those pop out slats from the back of the case you pop out for the gpu to stick through. front panel pop outs for cd drive and so on. basically anything and everything they may need/want in the future.
he'll be happy to have it all in one spot and can go through it if/when needed.