Hiya! Bunnies hump each other, including on the wrong end, to assert their dominance, as well as for frisky behaviour. Even neutered males get a bit frisky at this time of year, but as you are bonding, it is more likely that the majority of this humping is him telling her that he is in charge.
Are you separating them frequently during the bonding, or have you just left them together? I suspect that you are doing short sessions, and this is probably why the humping is persisting. Every time you reintroduce them, he will have to start all over again. As you haven't seen any other aggression, I would be inclined to put a day aside and supervise them together all day. He should stop humping her eventually!! If he humps her head, gently take him off or clap your hands to make him let go, because she could give him a nasty bite on the privates :shock: Other than that, unless there is any aggression, just leave them together and by the end of the day you should have bunnies well on the way to being bonded.
If you're not happy about putting them back into the same hutch/cage at the end of the day, I have been known to leave them together in the kitchen (neutral territory) and sleep on the floor nearby so that I wake up if there are any disturbances! If you're eventually putting them together into one of their existing houses, preferably use the males one, as he will be less territorial over it. In any case, move it around, move the food and water, disinfect it, basically anything to confuse the existing occupant that this is "their" territory - then they are much more likely to accept the newcomer into it.
Good luck, sounds like you're doing great!