As you say it is too late to file an amendment. It looks impossible to claim a refund because of your prior error in cost basis. Per the IRS:
File within three-year time limit. Generally, to claim a refund, taxpayers must file a Form 1040X within three years from the date they timely filed their original tax return or within two years from the date the person pays the tax – usually April 15 – whichever is later.
You can make a case for a basis change if you have two items of fact: (1) proof of purchase date(s) for the remaining 100 shares and (2) stock price(s) for the stock purchase date(s). These you might get from
a lookup on Yahoo Finance, Morningstar, etc. If you can't find stock prices on Yahoo, Morningstar. etc, try writing the company you own to get historical prices form them.