Can I apply a retail code to an account that already has a retail code applied? I only applied this code from COH GR AFTER Freedom was launched. Do I still get the same benefits as a VIP, the costume pieces, powersets and reward tokens?
You can apply multiple retail codes to City of Heroes accounts that already have retail codes on them, within some limitations. (For example, I do not think you can apply multiple copies of the same type of retail box on a single account, so if you have already applied Going Rogue to your account, you likely cannot add a second Going Rogue code but may be able to add an Architect Edition code.)
To answer your question specific to applying Going Rogue after Freedom, I found this City of Heroes forum post that describes what you get in great detail. But to summarize here, you would get: