Where was his partner for these situations? I wouldn't ask the C about CI although I have to admit it's a bit tougher to call with the "sound" of the BBCOR bat... With BESR it was pretty clear <thump> or <tink>. Unless I'm 100% sure I hear it, the C screams in pain, or the C glove ends up 10-20' down the line :-), I'm probably not calling it. If it's just a grazing and I miss it, I can live with that. If it was painfully obvious and I miss it, shame on me. Partner probably could not hear or see it either, but doesn't hurt to ask him if you're questioned.
As for baseline violation, northtxump has a pretty good summary. I've always tried to position myself for angles so as to not miss the tag. I also try to stay on the opposite/diagonal side of the play that my partner is in (think a rectangle and opposite corners). If on the tag attempt the runner makes a juke so wildly obvious and it's on my side, then I'd have an out. I've been taught to consider the fielder as well - was it a wild swing of the glove or was it a step and reach by the fielder *and* the runner moved further from that at the same moment. If the runner was already outside of that reach, then was he making a direct line to the base? Lots of stuff to decide in short order and for me has nothing to do with cleat marks - whose cleat marks are they, when were they made? Does someone come out after every play and rake off all marks? (can I have that job ;-)).