"How did the computer system know about the Doctor, that Eleven used to like wearing a fez?"
This is answered in show, you must have missed it. She says "I don't remember ordering anything. Must've been a while back". The inference is that it was the 11th Doctor who ordered a fez. Note that The Doctor is not surprised at the Kerblam! delivery droid entering the TARDIS - she is both aware who he is and doesn't seem phased that he entered the TARDIS. Like real-life Amazon, who are currently trialling a system whereby they can enter customer's houses in their absence, it makes sense that The Doctor has pre-approved Kerblam! to deliver to The Tardis, so she must be a customer and the order was likely a genuine one.
"[How did the computer system know] where (and when!) to find her current incarnation?
The delivery by Kerblam!, apparently thousands of years after the 11th Doctor ordered it (remember all the time he spent on Trenzalore) reminds me very much of the Red Dwarf episode "Better than Life" in which a mail pod had been tracking the ship since it left Earth three million years earlier, and since the ship has now turned around, the pod has finally caught up with them. The Doctor travels through time and space, so any delivery would have a great deal of difficulty finding the TARDIS. I doubt it would actually have taken 1000 years to fulfil the order, so it makes sense that it has taken all this time just to deliver it.
The delivery actually caught up with the TARDIS inside the time vortex, so it must use some "cheap and nasty" form of vortex manipulation, but inside the vortex is not a particular time or place in history, so really the delivery droid didn't know where in time to find the Doctor. It seems that the encounter inside the vortex was just a chance one after a very long time tracking the TARDIS across time and space. And of course, being a time machine, the TARDIS could visit Kerblam! at an appropriate time to respond to the cry for help.