you should send out your app asap and add the new lor later. The med schools give you plenty of opportunities to update your information. The majority of schools send out a secondary invite before even reading your initial so that would be a great opportunity to talk about your new clinical experience with the md. And i think that the lors from the dos should be helpful because med schools are looking to see that you have had patient contact and that you know what you are really getting yourself into.
thank you!