If they’ve not actually rebuilt your bike up, I’d just ask for it to be built back up with the parts it went in with, unless there is something specific required (new headset etc.. as you’ve mentioned). Or as ^^ nedrapier says “if they have binned them, rebuilt it and can’t return them or prove wear, you have a bit of haggle room”.
When I got my frame warrantied, the bike shop were very clear as to additional parts I needed such as new cables, invisi kit, a brake bleed (internal routing) and headset before it was rebuilt, which was an agreed cost. As was the £75 rebuild of my parts onto the new frame. I had asked for them to build it up with everything else off the old frame, even though I knew/they knew the drive chain, tyres and pads were worn.