This is almost silly, so I’ll be surprised if it works flawlessly, so far though it seems to work well enough. :-)

I got Twitter Tools to work with identi.ca by modifying the file twitter-tools.php so that the URIs used are:

define('AKTT_API_POST_STATUS', 'http://identi.ca/api/statuses/update.json');
define('AKTT_API_USER_TIMELINE', 'http://identi.ca/api/statuses/user_timeline.json');
define('AKTT_API_STATUS_SHOW', 'http://identi.ca/api/statuses/show/###ID###.json');
define('AKTT_PROFILE_URL', 'http://identi.ca/api/###USERNAME###');
define('AKTT_STATUS_URL', 'http://identi.ca/api/###USERNAME###/statuses/###STATUS###');
define('AKTT_HASHTAG_URL', 'http://search.identi.ca/api/search.json?q=###HASHTAG###');

Hopefully this is all that’s needed :-)