I honestly think the reason why Eva never brought up what she saw upstairs is because Shane probably told her what we hear in his confessional from him and her; Not to bring it up and cause everyone to panic right now, because he planned to tell everybody the situation later on. And then Shane dies, and now Eva's lost her alibi, because while she could just outright tell them what happened he's no longer there to confirm it anymore, and so it's entirely possible she thought that if she said anything with no Shane to back her up then people would've gotten even more suspicious about it and might've gotten even more blame put onto her - Disappearing with someone for a while, lying about it, then that other someone dying and then only AFTERWARDS when they're dead bringing up something that only you two saw and nobody else can confirm is pretty sketchy to be fair. The others may've voted her in because of that, or wound up isolating her from the group which would've allowed Sarah an opportunity to kill her off and remove the final witness without the others getting in the way.
It's also very possible that she just never had a good time to ever bring it up properly to anyone; Everyone, including Eva herself, was focused on just keeping themselves alive, solving the puzzles and clues, and making it through without going into a Death Challenge. Not to mention the fact the House Staff were almost ALWAYS lurking around them, whether it was just Arthur, just Sarah, Arthur AND Sarah, or all three of Arthur, Sarah, and Marvin. There wasn't much down-time for any of them, especially completely alone, so maybe Eva just could never get the right moment where she wasn't focusing on something else important.
As for whose body it was, I used to think when I first watched ETN that it was the driver of the car who brought them to the Estate, but watching it back again it's definitely not since the driver is seen WITH the car at the end of Ep.1 and gets killed in the explosion (though honestly I think the person that Sarah killed SHOULD have been the car driver).
So aside from that, my best guess is that it was another Society Against Evil member; Shane went in there KNOWING what was going on and hoping to banish the Evil of the Estate, and in his note he also makes explicit mention that the SAE has marked clues to help the Guests with the symbol of the group. Shane can't have put those marks there, he didn't have the time for that whatsoever. So I think that it was a Society Against Evil member who had snuck onto the Estate prior to Shane and co all arriving to survey the location and mark whatever was necessary in order to help, and then likely as he was going to leave to allow Shane to get things done on his own accord (Shane is probably a newer member of the SAE tbh) Sarah caught him and killed him.
Joey very likely didn't know, and I imagine the most likely reason why he said "no snooping around upstairs" is just because of a privacy thing, since it's his home. But alternatively, since Shane does mention that Joey has a look in his eyes that comes off as though he's hiding something, it could be possible that Arthur, Sarah, and Marvin knew that this SAE member was snooping around and getting up to things, and Arthur told Joey "hey, we have some issues going on upstairs, don't worry about it though because we're resolving it, just don't let any Guests go roaming so it can be handled". And so Joey said to everyone to stay downstairs "for dinner", all while looking a bit shifty because he knows there's something going on upstairs but hasn't been told what.
