Music13 tax extension expires today. I do not have all the documents to file a complete return. Should I just file with what I have and then amend it later?

Yes. You will be fine as long as you paid your tax liability. 

@rr1529 

if you are going to be due a refund, I would WAIT and not file until you have everything.  That avoids the amendment headache. 

if you think you will owe, I would go to the IRS website and make a payment tonight.  Make the payment high enough so you are due a refund once you file.  Then I wouild hold off filing until I had all my documents (why don't you ahve them all????)

there is no penalty for late filing if you are due a refund. 

there are penalties if you owe and if you owe, there are late filing penalties as well.