There are no such pornographic stories involving Amy from Doctor Who. The show focuses on adventure, science fiction, and positive storytelling, not anything of an adult or inappropriate nature.
Possibly, it's a story where lemons have some magical or symbolic significance for Amy and the Doctor, leading them on an unexpected journey through time and space.
I'm not very familiar with this specific 'amy waldroop gracie's choice true story'. It could be a very personal or a relatively unknown real - life account. Maybe it's about a person named Gracie and her choices in life, with Amy Waldroop being somehow related, perhaps as a narrator or a key figure in the story.
Yes, you can find Doctor Who fanfictions that have Amy Pond pregnant. Fan writers often use this idea to add new dimensions to the characters and the story.
You can start by looking on popular fanfiction websites like Archive of Our Own (AO3). There are a vast number of Doctor Who fanfictions there. Just use the search bar and type in '11th Doctor and Amy kiss'. Another option could be FanFiction.net. However, the quality and content can vary greatly on these sites. You might have to sift through a few stories to find one that really catches your interest.
There's also a chance that a new, original villain could be created for this fanfiction. It could be an alien race that has a grudge against the Doctor for something she did in the past (even if it was a past regeneration). And they target Amy and Rory to get to the Doctor. This new villain could have unique powers and a complex backstory that makes them a formidable foe.
It usually involves more explicit and adult-oriented scenarios between Doctor Who 11 and Amy. But be warned, such fanfiction might not be suitable for all audiences.