Brendan, I think 2 down is a 6-letter word meaning "studded" minus its first letter - the answer is also a common nickname for people called Clarke. The penultimate unchecked letter is a B. I had an L for a while but it won't parse that way
31 across - key on computer + Biblical floating vessel minus final letter and yes, the penultimate unchecked letter is A.
Good point about the clash resolutions. I put in the Greek letters but on reflection "the same symbol" suggests the English letter.