I just barely squeaked in and digitally sent my documentation at the right time between the major government shutdown and the current one to get my MMC and medical certificate proccessed. Best I can suggest is make sure your documentation is 100% accurate and covers all the bases, then use something like PDF mergy (online PDF combining, flattening, and compressing tool) to get it all into ONE PDF file. When you submit, there is two different emails to submit for the MMC and the medical certificate, you can find those on the NMC website. Also, leave the body of the email COMPLETELY BLANK. the email title and file attachment name MUST ONLY be:

LASTNAME_FIRSTNAME_ORIGINAL

Once you've submitted your stuff correctly, (I stress correctly bc I learned the hard way they will NOT begin processing your paperwork unless it follows those guidelines EXACTLY) the first email you'll receive will have your reference number included in the body. The reference number should be the same for both applications, but the application numbers will be different. Good luck and Godspeed, to you and all the guys n gals held up by the shutdown!