The big problem is that he left Harry his wand. If he uses more precautions against Harry, but still keeps leaving Harry his wand, then that makes the fact that he left Harry his wand less realistic, not more. So I actually think that you should go the other way with it - have him be less paranoid about Harry. Because otherwise you're making the inconsistency even worse. He's being cautious and paranoid enough to strip Harry's clothes from him, but leaves the wand in Harry's hand for one moment longer than he has to? It makes more sense if he has the Death Eaters throw a bunch of Finites at him to check for residual traps left by Dumbledore, and for that to be where he sees most of the threat coming from.
This.
Voldemort's not only being paranoid enough to strip Harry's clothes from him, he's being careful and cautious enough to remove an object Harry Transfigured without letting their magics interact. That kind of attitude is jarringly inconsistent with leaving Harry his wand for no apparent reason.
Luke_A_Somers already suggested adding a reason for Harry to have his wand. I think that adding such a reason combined with changes that increase our estimate of Voldemort's estimate of P(Time will try to thwart Voldemort's attempt to avert the prophecy through...
This is a new thread to discuss Eliezer Yudkowsky’s Harry Potter and the Methods of Rationality and anything related to it. This thread is intended for discussing chapter 114, and also, as a special case due to the exceptionally close posting times, chapter 115.
There is a site dedicated to the story at hpmor.com, which is now the place to go to find the authors notes and all sorts of other goodies. AdeleneDawner has kept an archive of Author’s Notes. (This goes up to the notes for chapter 76, and is now not updating. The authors notes from chapter 77 onwards are on hpmor.com.)