doctor who - Did the Pandorica rebooting the Universe do weird things to Rory?

In Cold Blood, the episode where the real, legitimate Rory dies, he dies because Restac shoots him. Then, of course, the cracks in time absorb and erase him. As far as I can tell, the cracks have nothing to do with the drilling that wakes the Silurians, or anything else that relates to the plot, except for Rory's absence of existing

Auton! Rory, of course, isn't a living, breathing Rory, so we'll forget him for the moment.

The Doctor reboots the Universe by allowing the Pandorica's restoration field and the preserved pre-explosion Universe atoms to shine across all of space and time, thus undoing the TARDIS explosion, and restores everything to the way it was before the explosion.

The problem is—

Rory wasn't killed because he walked into a crack—he was shot by a Silurian.

Shouldn't he be dead, but now remembered by Amy? Alternatively, if the Pandorica's restoration field brought him back to life, shouldn't it, by virtue of shining across all space and time, not have allowed anyone to ever die?

Assuming that

New Rory isn't a Auton/Flesh/etc. duplicate, if the Pandorica did manage to restore living Rory to the state he was before the TARDIS explosion, then hasn't he gone on all the adventures that he previously had already?

So why did the Doctor say that Amy/Rory's wedding night was the first time he had been on the TARDIS in "this version of reality?" Did the Pandorica screw something up?

Comments

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What is the etymology of Doctor Who?

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