I'm in a similar situation: I withdrew 4k from my IRA in April. I didn't end up needing it but held on to it until now, and I wanted to redeposit the same amount on top of the 5500 I put in last month. I sent Vanguard a message explaining this and they said:
An indirect rollover can be processed by withdrawing the money from your IRA account and redepositing the same amount back into the same IRA or a different IRA within 60 days. If you hold the money longer, it will be subject to taxes and penalties. Under revised IRS rules that went into place this year, you can make only one indirect rollover in a rolling 365 days, regardless of how many IRAs you own. You have passed the deadline to complete an indirect rollover.
I thought I could withdraw principal penalty-free at any time, since it's already been taxed...? I'm going to call them to see if there's anything else I can do, but thought this info would be relevant to you in the meantime.