When bonding any animal, it is better to leave a periof of time whereby you can start the bonding off and not split them and leave them together. This allows the bond to be created and held rather than keep splitting and confusion the animals. Unfortunately splitting and rebonding animals is more stressful than doing it all in one session. Personally I will not start a pairing up unless I have at least 48 hours straight to get on with the bonding without any reason to need to go out. If you have not got this time free, it is best not to start bonding but to leave it untill you have the time.
My advise would be on your next time of putting these together to then keep them together and then transfer them in to his hutch which will have been thoroughly cleaned with a strong smelling animal friendly cleaner, vinegar is also perfectly acceptable as long as it is allowed to thoroughly dry before placing them in their new appartment. Once they are put in the hutch do not separate them, if one needs to go somewhere like the vets, take them both. You may find you get the same initial chasing, humping and nipping occur when they go in their new appartment, however you need to consider that whereever new they go you will get this. To forge their bond they need to go through this.