I funded a ROTH IRA in 2016 to $5500 & recharacterized $4400 to a traditional IRA today to stay under the limit.Do I list only the $4400 as recharacterized if I had gains

[dmertz]

Yes, that is correct.  You recharacterized $4,400, but more was transferred due to earnings that were required to accompany the amount that was recharacterized.  Box 1 of the Form 1099-R reports the amount transferred, not the amount recharacterized.  Your explanation statement should provide the details, including the amount that was recharacterized.