I don't like the one foul ball after strike two idea. I think a hitter's ability to foul away borderline strikes to stay in the box for another pitch is a skill to not be punitive. I think it goes along with the idea that you don't abolish the shift, you expect the hitters to deal with it and hit away from it. We are probably biased, but we wouldn't have the Dave Bergman at bat in our memories if this rule were in place. An at bat that gets extended in time by foul balls also gets a shot of adrenaline with each pitch. I think that adrenaline is what people find enjoyable while watching a game (the actual foul ball, not the 30 seconds of unnecessary wandering around the mound and batting glove adjustments that might come along with it).
As far as calling time outs and being back in the box, etc, if a batter doesn't move their feet on a pitch, there shouldn't be much of a delay in between pitches. Heck, even if they swing and stay in the box and maintain balance, there shouldn't be much delay. A pitch up and in that pushes a batter back and out of the box, you have to be reasonable. A batter gets a bug in his eye or a contact comes loose or something like that, you've got to acknowledge those issues come up. I think umpires probably have a decent idea as to who is milking it in those situations. You have to give the umpires the power to keep things moving along. (And, yes, I realize I am lumping Angel Hernandez into this using good judgement scenario, but I didn't claim my idea to be fool proof.)
As for the in field non pitching mound visit conferences, put a limit on those like mound visits?