Letting AJP pinch hit had to be some kind of matchup thing. AJP is not really a good enough hitter to warrant a PH appearance except in specific matchup or desperation circumstances. When you then pinch run Sizemore, it does make you wonder why Sizemore didn't just pinch hit in the first place, as noted. It worked out pretty well, but largely because AJP made really crappy contact - it's not like he hit a rocket down the line.
Small sample size always applies, but with WMB and Victorino unavailable, the bench empties quickly. You really don't have much choice but to PH for Roberts in late and close, but that requires two bench players since you also need to sub Herrera in the field. WMB will be back soon, but part of me wonders if Cecchini will get a shot the next time this comes up, especially if he stays hot in Pawtucket (it's only a week, I know). They could really use a guy that they don't need to PH for at 3B, especially once you add in all the platoon (dis)advantage they experience.
Also, while second guessing is supposed to be about the managers - I was at that game and I second guess the intelligence of having 4:05 games at Fenway. The sun glare was horrific and getting to the ballpark sucked (it was still half empty when I arrived there at about 4:45). As well, they stopped serving beer at essentially 6 PM which is just when you want one. Keep them at 1:05 or 2:05. Sure you have to take a half day from work and/or pull the kids out of school, but that's half the fun of weekday day games. 4:05 is like one of those things where you compromise by making everyone unhappy.