To disclose or not to disclose?

Could use some advice...

Back in the late 90's I opened a 401k for my solo consulting company. That 401k had Money Purchase and Profit Sharing Keough accounts at Fidelity. At some point in the 2000's the combined values of those two accounts exceeded $100k (neither was over $100k) - I believe it was the year before the limit increased to $250k for requiring 5500's. I wasn't aware of that requirement and didn't find out until years later when I closed that consulting firm. I then got a bit freaked out about the possible penalties and just left the accounts sitting there. Dumb, I know. 

So, I need to finally deal with this. Can you confirm that it was the combined value of those two accounts that triggered the 5500 requirement? or did each account have to get to $100k? And if it is the combined value, how would you proceed? Send the final 5500 and hope for the best? Do the DVFC and pay the fines? Tear-stained letter begging forgiveness? Other options?

Thanks in advance for any guidance... 

It was the combined value; the limit for 2006 was $100k, the Pension Protection Act increased the limit to $250k for 2007.  But that is a very long time ago... it would be very hard to have maintained accurate records going back that far, especially when you consider the damage you took in the fire/flood/earthquake of 20XX... or were those in the files your kids accidentally tossed when you told them to clean the garage...

If the accounts now total over $250k combined, I'd start with the 'Final' 5500-EZ; and "as many" previous years as you have "sufficient" records for.  The IRS correction program (not the DOL's DFVCP) caps the penalty at $1500 per plan.  [Although I'm perplexed by your statement that the 401(k) PLAN had profit sharing and money purchase Keough accounts.  Yes, previously two plans were needed to get to 25%, but they could have been merged under one document anytime after 2001(?).  The monies can be in multiple trust accounts and still be part of one plan, so I don't know if you still have two plans to file for or not.]