The bunnies are officially bonded!! 
The whole process took about 8 weeks in total from the day we brought Leo home until now when I can say they are completely bonded.
Even though I'm still new to having a pair and have only gone through the bonding process once, I'd like to comment on somethings I've learned along the way.
First of all, I was skeptical at the bunny dating... Arduina didn't seem interested in anyone (she tried to fight/nip at every bun). However, Leo was friendly toward her (lowering his head in front of her wanting to be groomed, ie not fighting back) so we decided to bring him home.
The first week or so they did ok running around the neutral downstairs bathroom. We had some issues with neutral space in that Arduina thought the whole house was her Queendom (she wasn't allowed in the downstairs bathroom and had only been there once when she was a baby). When we had a new house mate move in downstairs we moved them upstairs and thats when the big fight broke out. Leo was in Arduina's territory.
Breaking down Arduina's Queendom was probably what slowed the whole thing down. Not being able to keep Leo in Arduina's room put a damper on things until we needed the room as a guest room. We moved her out into the living room with Leo. From there they had separate play times in the living room and bonding each night for ~2 hrs.
We progressed as much as the bunnies wanted to. For example, when Leo or Arduina tore down the cardboard surrounding the other one's pen, we knew it was time to take it down (they originally fought through the bars).
The turning point where things started to pick up quickly was in the box (big green tupperware container) when we stepped back (not quite so literally). Instead of petting them to calm them down and keep them from not fighting, I would shake the box if one of them started to pick a fight. Arduina learned quickly and completely stopped nipping at Leo. Leo took the upper hand and we would then use the spray bottle on him. I did this in the bathtub and when they were more focused on trying to jump out of the bin then trying to fight with each other, we moved up to the bath tub. Same in the bathtub, when they were more focused on jumping out of the tub then nipping at each other, we moved up to the bathroom.
Once they were able to run around the bathroom (now neutral) with no fighting and we saw some positive interactions (licking and eating together). I had them spend two nights in the bathroom (I'm a light sleeper) with the door barricaded. After that I took the larger (4x4ft) pen and washed it really good and set up a neutral pen back in the bunny room (they hadnt been in there in 4 weeks or so) with a brand new tarp as the floor covering. I spent the weekend with them, and they did great, no fighting whatsoever.
In conclusion:
Progress as they are ready (once more focused on finding a way out than nipping/fighting, move to the next step). Also, plan your next two steps ahead of time (it may come sooner than you think!).
Sometimes stepping back (aka not interfering) helps them sort things out, either shake the bin/cube their in or use a spray bottle (shaking worked to stop Arduina while spray bottle worked for Leo).