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How do the Doctor's enemies keep track of which Doctor is which?
Doctor Who zips all the way up and down through time, popping in at any time and place. If you don't have a time machine to follow them around with, it should be impossible to keep track of which incarnation was where. And yet, the Doctor's enemies somehow manage to do just that, with the Daleks being accurate enough to determine he was on his last regeneration on Trenzalore.
How much of a TARDIS is essential to its function?
While we hear of the TARDIS having engines that are implicitly essential to it working, we've also see a TARDIS work without the rest of the machine.
"The Doctor's Wife" and "Inferno" show that a TARDIS is capable of operating as just the console, which would seem to imply that they're just a power source to allow the console to do its thing and move the whole ship around, or to allow for the pilot to do silly things like tow an entire planet one second out of phase.