I would not submit anything to the USCG/NMC until I was certain that all known requirements have been meet. In your case, you know that you have some training outstanding. Why would you want to submit an application when you know that you do not meet the requirements? My suggestion is that you finish the training and all other items on the checklist before submitting anything. It helps you and the USCG that way.
As far as your sea service goes, it should be evaluated the same as before.
Good luck on your exams.