You usually have until they are 10-12 weeks old before you need to separate until they are spayed/neutered. I waited til 12 weeks and was fine. Even if he does get his hormones in before 12 weeks, females usually can't get pregnant until at least 3-4 months old at the earliest. Though if his hormones come in and he starts pestering her too much, then you should separate. At the latest I would separate when she is 12 weeks old and him 11 weeks, though safest would probably be 11 weeks for her and 10 weeks for him, and I would put them in cages/pens next to each other to try and maintain their bond as much as possible. You won't be able to get him neutered until his 'plums' drop, and the exact time for that can vary with each rabbit, usually 4-6 months old.
As for her being scared, it could just be her adjusting to having a new buddy, or sometimes when they get past their baby stage and reach puberty they start to get a bit moody about things, particularly females. It could also be that she wants to spend time with her bunny friend for now and is worried about being separated from him as he makes her feel safe. If that's the case I would just spend time with them by sitting with them in their area while they play, and not fussing her if she doesn't want it, in particular not picking her up as that is the thing most rabbits hate and picking up can affect their trust in us the most. This also might be why she has started running away from you if you pick her up very often. Just sitting with them and not bothering them when they don't want you to, will help strengthen your bond with both of them. Just give it some time. She may settle down as she readjusts to the changes and you spend more time with them, or it may be you will just have to wait out the dreaded teenage phase that some go through.
This link also has some good tips on bonding with your bunny.
Also reexamine any scented products you use: eg. lotion, shampoo, hand soap, etc. It could just be a scented item you are using that she has decided she doesn't like the smell of. Rabbits have very sensitive noses, so it's not uncommon for this to happen.