Hi BarkingPup, thank you for your reply

Here're the answers to your questions:
1) neither were spayed/neutered. As Flipper was ready to mate, I decided to adopt his mate.
2) Raspberry and Flipper, once they cuddled and started rubbing their chins on each other, were put inside a new carrier (neutral territory) and then taken to a groomers and the vet. They were kept in the carrier even after coming home. Flipper mounted her after an hour, and she was relaxed. Then they were allowed to exit the carrier and welcomed to Rasberry's new surroundings.
3) Raspberry's previous conditions: horrible. She was in a cage with at least 25 other rabbits, it was dirty and the rabbits were all frightened half to death by everything. The institution did not have anough funding, and Rasberry's wound had possibly been aflicted by aggressive (and much larger) bucks.
4) As they were both rescues, I am not certain of their age. I estimate Flipper to be a year and a half, and Raspberry to be about 8 months old. Both definitely very young.
I have been referring to the House Rabbit Society for a while, and do indeed find them extremely helpful and to offer excellent advice

Thank you for recommending them.
Here's an update of what has happened since I posted this:
I spent an arm and a leg and took them to one of the best vets in the city as I did not trust the previous vet's advice on "it's ok to keep them together". It turns out that Rasberry's wound, although healing externally, had actually destroyed her vulva. She is scheduled for surgery and will have the scartissue and wound surgically removed to ensure that a clean wound can heal there instead.
This would explain Rasberry's behaviour... because even though she was given free reign of a large, 3-storey cage and Flipper was kept outside, she and Flipper were extremely affectionate to each other through the bars. Raspberry was very docile every time she was picked up, and I have been working with her petting her, cuddling, feeding her, speaking to her and putting her at ease. However, she would suddenly freak out and quiver due to no reason I could attribute (noise levels, etc,) so I even suspect she's slightly bipolar due to the abuse she suffered.
I have also been working with Flipper who is obviously enamoured but frustrated at not being able to go near her (I wanted her wound to completely heal since I assumed it may have been hurting her after the first time they mated). He is currently heartbroken and mad at me for having left Raspberry at the vets so I am doing my best to shower TLC on him as well.
Do you have any reccomendations on how I should proceed after their surgeries? They will of course be kept seperate for 2-3 weeks until Flipper's hormones settle and Rasberry's wounds heal completely and the stitches are removed.