I would wait to bond them until she is spayed as well. Her hormones can cause as many problems as his would when it comes to bonding. You also need to make sure he doesn't have any viable sperm left. It can take 6 weeks for all the sperm to be gone, so he can still get a doe pregnant during this time. Even though she may seem young when he is done, some females can have litters when they are 3-5 months old. This is probably rarer for a Flemish, but it is still better to be safe than sorry.
You can try letting them have play time together and work on bonding, but I would not have them living together until she is done. If you can get her done sooner rather than later, the hormones should not get a chance to settle in, so it should take less time than if she is allowed to get more hormonal. I am not sure what the best time would be for a Flemish, but they do mature slower than smaller breeds. Getting her done at about 5-6 months would still be good.
They should be able to live together, but it is best to wait until both are spayed or neutered.
When they are bonded, you need to make sure there is enough space for both of them. They are big rabbits, so would need a huge cage or space. I would probably do at least 2.5 times what a single would need so both can have enough space. You will also need to find a suitable carrier. Bonded pairs should go everywhere together, preferably in one carrier. Since Flemishes can be quite large, you will need a big carrier or 2 wire ones you can put beside each other. If you do get 1, make sure you can lift it. A possible 40 pounds of rabbits is going to be heavy and might not fit easily in a car.
