Is there an easy way to add comment numbering (i.e. each comment in a post is sequentially numbered) so that comments can easily be referenced. Many thanks for such a great theme.

Unfortunately only on a per-page basis, i.e. the numbering would start again on the next page. The comment numbering and pagination was better in Atahualpa & WP 2.6 with the plugin paged comments (except there were no threaded comments). I think WP is still improving the new comments features and there's also room for improvement in the Atahualpa implementation. I hope to include numbers and separated pings in addition to indention, threading, pagination and reverse order, in the next versions

This could be a case of the blind leading the blind but …

I use Greg's Threaded Comment Numbering. See this thread where Flynn helped me out.'

http://forum.bytesforall.com/showthread.php?t=1303