I can make some summarizing again if you don't mind.
1) I'm sure investigators, contrary to pprune detectives, has all photos of all parts of plane and some of them have plenty of time to look at them at site and even touch them with their own hands. So there is no "mystery" of lost part of HS and VS (for them, or we will know).
2) We cant beat them in game "look we found some suspicious holes, it's a bomb!" so if there was clear evidence of explosion it will be found and nailed already.
3) There is no clear evidence of the way relaxed security at SSH make bomb planting possible or we already will read about suspects arrested.
4) All other "clues", such as sat surveillance, phone intercepts etc. are too weak to make case strong enough to pinpoint it. They can however add flavors after it will be solved through other means.
Major mess organized in Egypt by other countries in my opinion can be not directly driven by any proof but by the fear that in current conditions - even if this was not terrorist case - bombing can be easily made. For example, if you found that your jewelry was stolen, you will check locks and latches and repair them immediately, asking somebody to guard your house till you will go to hardware store, even if most probable case was that your housemaid stole them.