Re moving the bodies, provided the markers sticks have a ref number which is repeated on the body bag, it will be possible to see which part of the aircraft they were seated in.
Any tampering with bodies, like removing shrapnel will be evident at autopsy.
Re who did it, I think if the rebels knew it was the Ukraine forces they would have had a secure cordon in place immediately, nothing would have been touch and the experts would have been allowed and escorted for safety ASAP. They are not stupid and would not have wasted such an good propaganda opportunity.
Yes we saw collections of passports and bank cards etc but how do we know at this stage they won't be handed over to the investigation team, after all they have been witnessed with them and didn't confiscate the film.
Personally I believe it was a rebel c*ck up, but now their initial panic is over are they likely to make their position worse by holding on to these items, after all the pax list is known so it is easy to get the passports and cards cancelled.