For the second year running, my electronic filing has been rejected for code IND-901 - the IRS thinks I'm dead. Had anyone encountered and solved this?

Error code IND-901 is usually caused due to a Social Security Administration error. As you stated, they provided you with a letter. Did you provide the letter to the IRS? Also, I would contact the SSA again and make sure they did what they were supposed to do on their end to clear this error.  

You should check with the Social Security Administration to make sure their records are accurate. And make sure the IRS has also updated their records to reflect this.

A return will reject with code IND-901 or IND-941-01 when IRS records indicate that the person identified as the primary taxpayer or spouse on the tax return died prior to the tax year shown on the return.

The Primary SSN in the Return Header has been locked because Social Security Administration records indicate the number belongs to a deceased individual. Check the primary taxpayer's name and social security number against the actual social security card.