If you look at what Shepard's body looked like when they were rebuilding her/him, there are a LOT of gaps in bones and so on. I'm betting they had to use some cybernetics in the places they couldn't regrow bone or so on. (This isn't Harry Potter, after all.) As for eyes... eyes are REALLY tricky. If you listen to all of the audio recordings in the very beginning Ms. Bugs Bunny, I mean Miranda goes on about how they moved on to some kind of new type of regrowing and making parts. (I could be wrong, I was tipsy the last few times I did that part, but I do remember it was not normal and had moved onto something else that 'showed promise'.) With all of the nerves and doohickies that make eyes work, I wouldn't be surprised if they had to monkey around with some cybernetics to make a pair that worked properly again. But eh, that's just me.
I mean, if we're going to call on all of the plot holes, why don't any of the mercs in the ArchAngel mission care that I'm wearing N7 on my armor? (Or running screaming if I'm wearing the Collector armor, which I never do because of the GOSH DURN HELMET!!!!) Or why doesn't the Asari Council member just vulcan mind-meld or whatever with Shepard like Liara did to see her bloody memories to find out about the 'reaper' thread? Or....
I'll stop now. Needless to say, we're expected to take a few things with a bag of salt. Haha. (Like, Shepard would set of every metal detector in the galaxy with all of the metal she has in her to piece her bones back together... she was messed UP, man.)
I never practiced my signature with an intended target's last name... I actually cast my entire class in the Phantom of the Opera musical with my desired target as the Phantom. I spent WAY too much time picking through who would be who.... Sad sad little creature that I was. /shakes head