I imported ~30k hands which took around 10 mins. Then the window "Clustering PokerTracker 3 Beta" came up and is still running about two hours later. The Import status window seems to imply that the clustering is complete though.
From the import window:
2008/02/06 12:25:29: Import beginning
2008/02/06 12:25:29: Converting PokerTracker v2 Database: PT_R_LPTP
2008/02/06 12:25:29: Retrieving hand count from database...
2008/02/06 12:25:32: Database contains 16,607 PartyGaming hands.
2008/02/06 12:25:33: Database contains 14,551 Full Tilt hands.
2008/02/06 12:25:33: Importing PartyGaming hands.
2008/02/06 12:31:14: + Complete (16,605 hands, 0 errors, 0 duplicates)
2008/02/06 12:31:14: Importing Full Tilt hands.
2008/02/06 12:35:45: + Complete (14,551 hands, 0 errors, 0 duplicates)
2008/02/06 12:35:45: Import complete. 31,156 hands in 2 files were imported. (0 errors, 0 duplicates)
2008/02/06 12:35:45:
2008/02/06 12:35:45: Clustering...
2008/02/06 12:42:15: Clustering complete.