I feel like I'm finally making progress on bonding Amelia and Cody. I took them to the Rabbit Club meeting this past Saturday, and they were in a pen together there for two hours with no problems. Plus being together in a laundry basket all the way there and back.
We purchased a pet stroller, and I think it's been a very helpful bonding tool. My current strategy is to give Cody a small dose of Rescue Remedy to help calm him down, then push them both through the house in the stroller for four to five minutes. I then immediately put them in a pen in a neutral area.
Cody still has a tendency to dart forwards towards Amelia, but he hasn't growled at her for awhile. He keeps asking her for kisses, and she has groomed his forehead VERY briefly for a few seconds, but most of the time she just sits there.
She is very comfortable around him, and I'm hoping he will get over his issues soon. Amelia is already about 8 years old, and she just wants someone to snuggle with. I'd like to get them into the nicer, bigger, more comfortable pen soon. (And then try to fix my wood floor that used to be really nice before Amelia expressed her annoyance at the bonding pen by peeing on the floor.)