Others may have done things differently, but I believe it is important to show just how far back your relationship goes.
In our case, my husband and I have known each other since fall 2001, and were good/best friends almost immediately. But we didn't actually become romantically involved until summer 2005, and didn't meet in person (i.e. officially start dating in person) until summer 2006. We included proof of our entire relationship though, as we believed it showed how our relationship has developed and strengthened over the years and how well we have come to know each other (and each others' friends and families).
Edit: I forgot to add that another benefit of approaching it this way is that it doesn't seem like (in your case) you guys have only just started to get to know each other 3 months ago.
As for the name thing, in probably 90% of the emails, chat logs, etc between my husband and I, he has always referred to me by a nickname he made for me back in 2002 or so. We just made sure to explain, in the section about emails and chat logs, who was who and why. I believe I explained the origin of the nickname in my handwritten timeline about the development of our relationship as well. It helps that there are also logs where we joke about it and references to my actual legal name, as well as gift cards from his family showing them calling me by both the nickname and my birth name.