
What a predicament, I can absolutely understand you wanting to stay on good terms with the breeder, but on the other hand I think she has changed the agreement. A pup for the stud fee means a pup. I've had several stud fee puppies over the years in 2 different breeds.
Way back (30+ years ago) when I was still fairly new to showing I did have a similar situation, I had booked a pup from a very successful, well known breeder (no relation to my dogs) and after the pup was born this breeder asked to use my champion dog on her champion bitch, I was really pleased and of course agreed. Back then it was common to get a pup for the stud fee and I just assumed this was the case, that it would transfer to the other litter. I travelled to the other end of the country when her bitch was ready, we mated them and I picked my pup up from the other litter. The breeder then asked me what my stud fee was, my dog had only been used once before and I got pick of litter for that, but I didn't have the confidence to say this as a young person fairly new to showing. I asked what she thought and she said she only charged £50 for her champions, my pup was £400 so I had 350 left to pay which was a huge amount of money for me back then. I didn't argue to maintain good relations but I learned the lesson to get things in writing, you may have to so the same.
As an amount I would suggest maybe £200/300 to cover costs.