If nobody else is responding, here is my personal interpretation of how the Home Office works: when they receive an EEA1/2 application, they put it on the shelf. They may read the cover letter, but I doubt that they even check the attached documents. They are very busy (or so they claim), so it will take a few weeks/months until they have time to look into it.

Consequently, you should send the application now (without the passport, or with a copy of it), to get into the queue. Send it by registered mail and keep the receipt, because the registration number is used as a reference. (It seems the Home Office gave up on handing out case references, probably because they are so busy...)

Once you are back, you have two options. Option one is to send in the passport, mentioning the registration number. You have to hope that they can reunify it with your application (which is likely, but not certain). Option two is to wait. Once your application is processed, the Home Office will be notice that the passport is missing, and will send you a letter asking to mail in the passport. In this case, the chances of application and passport coming together are pretty good, but you will loose some time (another week or two).