There are multiple (3) 5-year rules. The one you are referring to is, "Has he had a Roth account for at least 5 years?" It doesn't have to be this same account.

1099-R code T: "Note A code of "T" means the issuer of the 1099-R knows the recipient is over age 59 1/2 but does not know if the Roth IRA was held at least five years. So if the preparer believes this is a qualified distribution and the distribution is not subject to tax, they need to use code "Q" instead."

I don't know what this means: "But there is still sufficient funds in the account to cover his earnings." There are ordering rules to Roth distribution.

"I input zero in the taxable amount, since he has basis"

Does he have enough basis relative to the distribution? Have you entered his basis?