If I failed a background check, how hard would it be to submit a SF86 and apply for a secret clearance

If you want the best honest answer go to your SSO (Special Security Office) or your Unit's S2. They will have your answer. If you failed your investigation because of an error on your 86 they may be able to help you. If you lied then well again they may be able to help you. But those two resources will have the answer you are looking for.

As others have said, be completely HONEST about anything and everything and don't try to HIDE anything. Something may seem insignificant to you, but it may not be to the investigator. If they find a discrepancy or think you might be hiding something they will dig deeper and deeper.

I previously had duties as the Special Secuirity Officer (SSO) for the SCI folks and Asst Security Manager for non-SCI folks. To be honest some of the things i saw on SF86's made me wonder how some were still even in the military, let alone being granted a clearance. It was because they were honest and upfront about everything. Nothing to hide, no chance for someone to use it against you.

I used to be one of the many people that processed EPSQ's. NEVER LIE. It's ok to fuck up. Everyone makes mistakes in life. Don't try and hide shit. I processed a Full Bird COL with a DUI, I had numerous legal and financial cases. Shit happens. Everyone understands it. Problems arise when you don't fully disclose ANY situation. There are PLENTY of spaces you can type a narrative to explain your specific situation in regards to checking an embarrassing block.. DON'T TRY TO HIDE ANYTHING.