It is a common practice to withdraw in the following year, when the mistake is discovered, and just note that it was done on the 5329 when filing the "RMD missed" year.  The distribution always goes on the year of distribution, not the year of "shoulda."  

Gold has fluctuated in value from $1,377 to $2,342 an ounce in the last ten years.  If the IRA trustee hasn't been calculating the value each December 31, they at least should have been providing an inventory of what is in the account. You would be doing it wrong by using the current value of about $2,000 for the entire period.  

And how have the trustee fees been paid?