Okay as a fellow writer of Doctor Whooves I want to just say a few things, but i want you to know that I did like your story ^^ I especially like the fact that you have a credits sequence at the start of it (EQD rejected me because i had one and refused too loose it, but I like to see that some other pony had the same idea!)

First I want to say that you shouldn't flaunt your monster. Most people that read Doctor Whoof have seen doctors 9-12 and so when we make a reference to a ponyfied monster the visual is already pre made, but also so are the episodes they are featured in. The idea of ghosts haunting a morgue is very familiar to the episode the unquiet dead, and actually with your story its a bit of a retelling. Most of the time you want to try and avoid that. The writers of Doctor who are very talented and retelling an episode that they have already made only with ponies can be kind of boring to read. Always try to make the story yours, to stand out against not just the other Doctor Whoof writers, but also the writers of the actual doctor who.

The second thing i want to talk about is Pinkie Pie. particularly her lack of energy. Not seeing her friends for two weeks would be killing her under most scenario's and to actually see them again, she should be bouncing around going Pinkie crazy over them, but it feels like its toned down. I understand  this... because honestly i have the same problem with pinkie to the point where i tend to push her out of the picture at most situations. Don't be afraid to ramp out the crazy and hit that forth wall a few times with her, she will just bounce off and everyone can get a good laugh.

Third are your transitions. In a show we see the locations and scene's fade out and then fade in. In a fan fic we do not. Always try to bring a scene in with some kind of visual cue to let your readers know that the setting has changed. personally i prefer this one

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Finally Gallopfrey I have to mention this because I am one extremely jelly over the fact that I didn't think of that pun when i was writing my series, and second because Gallafrey is a very touchy subject to all Doctors. It is home world it's the world he destroyed twice, and it is a source of great pain for the character. To just bring it up on first introduction to me seems wrong. Especially if this is David's doctor who almost never talked about Gallafrey though i think with the timing of the episode this would be Christopher, but Pinkie mentions that he had changed, and dash had seen a regeneration. So I am actually very lost as to which Doctor is your Doctor. (I work with Matt personally, I despise him so it makes it easier to write)

also who does your tittle card? was it a commission and if so how much? did you find it if so where? I have been dying to get my hands on a picture for my series.