...does it mean anything that my Super Duper clone, which was made prior to these issues, experiences the same long boot time?
I'm not sure I understand what you're trying to say. If the boot delay on the clone is persistent and not seen only on initial boot as Jon stated, wouldn't you have noticed the delays on the main boot volume (which starts out identical) sooner? But it's a good point to realize that backups like Time Machine and clones may also contain MacKeeper files, just as there may be other, not MacKeeper-related problems hiding in the wings. TM in particular may need to be checked for MK and purged. Once that's done, it's recommended to fix permissions, and —if warranted— ACLs.
If permissions are OK, the next step is to identify other processes listed in Console logs during/around delays or time gaps in the logs. There are two gaps in the sequence you posted, around 3:07-3:11 and around 3:11-3:28. FWIW, the former is 'associated' with printer drivers and backup activity, the latter with backup activity and QuickTime. Time for a closer look at TM?
