Well, to begin with i'd first like to say that the way you have improoved in comparison to your first page is frankly startling! Even for me, a guy who had never seen a single episode of DW got hooked up almost instantly, but i could't get many of the references you made. The story follows the same universe as the one from DW, yet it has it's own charm, it's own style. Another remarkable aspect of this comic is the dedication you put in to make it look better, spendig long time watching over each detail, each background so as to nailed as well as you did. So, i'll give it a 10/10 for all the efford and skills involved.
I must say that even though I'm not a big fan of MLP (like it) and the whole Dr. Whooves things irked me when I first heard of it, you're comic changed my perspective. Yes, you still have the cuteness of the pony universe, but you actually focus more on the DW aspects. The story is interesting and is almost like watching an episode of the show except the Doctor is a pony (Weird, but believable). You also gave all the side character that are not focused on in the show depth and character that just makes you want to embrace the universe even further. Though your art style can be off at points, readers don't notice cause the story is engaging, and that's what's important.
Oh I duno. Regenerate, and have the new form finish it up with lyra and derpy? He won't be himself, but asuming he ggives one of them thhe details, it's just a matter of reading the manual for the next doctor. or the next doctor can just tap into his memory.