How many published papers should you have when applying to PhD programs?
You should be fine.  Realize that there are other kids coming out of liberal arts schools and going into top Ph.D. programs with almost no research experience.  And they do fine, getting into R1 grad programs, and producing work during Ph.D.  All of the kerflutter about undergrad research will fade into the background when you are in a real Ph.D. where there is sooo much more time to spend on research than undergrads (for whom it is a collateral duty...even if they manage to collect a few cap feathers).

Your application will consist of grades, test scores, letters, and other things.  Probably the importance is in that order.  We get kids all the time here who ask about overcoming the opposite worry (subpar grades and standardized test scores) by research.

Just do a decent job and apply to a few places.  You sound like quite a catch, really.  Also, realize that getting into good grad schools in the sciences is quite a bit easier than the whole hothouse environment of high school kids targeting Harvard.  Odds are much more in your favor.  The bigger question to consider is if you should spend more time in school or get a job.  But just put the whole ardent high schooler wanting to go to Brown mindset out of your mind.  It's a different thing, now.