Ok, first things first. I agree Harry (and Murphy) heights are probably just Jim being Jim. I think Paul Blackthorne was an excellent Harry even when he is not as tall as he should, but yes, I would not be surprised if a major company selects someone smaller. I laughed a lot at the Tom Cruise comment (by the way, TV show Reacher is quite good IMHO, but I have not read the book.)
Second, I agree with Mira the sentence about Malcolm means that Eb soulgazed Malcolm. Or perhaps it means that he saw him under the Sight, but I believe the first interpretation is more probable. Eb is a wizard, when he talks about seeing a soul I understand he is being literal. I also don't think he is talking bad of Harry's own soul. When he soulgazed him, Harry was not in a good place and I am pretty sure his soul was probably...undecided. Sort of Molly's. Besides, I personally think that Harry has a darkness in himself that Malcolm probably hadn't. I do not imagine Malcolm saying that he would let the world burn as long as Harry is with him.
Side note, we all wonder what people sees when soulgazing Harry, but I am wondering what wizards see when looking at him under the Sight. It must be scary, as I bet many of the Council did that and they do not trust Harry. Pretty sure they did not see an angelic paladin like Murph.
Finally, yes, there is a LOT that we do not know about Harry's mom, like how he managed to have Lea protecting Harry. I hope we find some answers before the series is over.