I can tell you what happened to me and maybe that will help. I submitted my primary around October and got my secondary shortly after that. I didn't submit my secondary until January. I rely on Veteran's benefits to pay for my schooling, and they couldn't understand why a med school would require two applications, so it took a while to get the funds. However, as soon as I sent it, I contacted admissions to let them know why I struggled to get it in. I can't say that it is beneficial to contact admissions for your problem, so do so at your own risk, but it may have helped me. Honestly, I didn't ask so I have no way of knowing if it helped. They are VERY friendly there, I interviewed recently and it is a very family/team atmosphere.
As for your D.O. letter, it is unfortunate that you waited to submit your secondary until after you received that, because they don't require that to submit your secondary, they only require it to keep your acceptance should you be accepted. During my interview day, they mentioned that they realize that in some places it may be difficult to get that letter, and they are more than willing to help people where they can in that regard. As for how full the class is, they mentioned they still have some seats available, but they are also interviewing for waitlist spots as well. I wouldn't be too concerned just yet, because they do interview into April and if you read the previous year threads for VCOM, people were getting accepted in February and even early March.
I hope that helped. Good Luck!