Dan, I'll offer commentary on two of the questions:
1. Is it possible that the readings were done by different labs? There are some labs (e.g. Epstein) that use the "new" Gleason protocol and others (e.g. Bostwick) that use the original standards. If your biopsy samples were read by a lab that used the "new" standards and your pathology slides read by one using the original standards that could account for the difference.
2. I would say your seeded friend was lucky. I had dark semen for a couple of weeks after both biopsy and brachytherapy.
Age 62 (64 now), G 3 + 4 = 7, T1C, PSA 4.2, 2/16 cancerous, 27cc. Brachytherapy 12/9/08. 73 Iodine-125 seeds. Procedure went great, catheter out before I went home, only minor discomfort. Everything continues to function normally as of 9/10/10. 6 month PSA 1.4, 1 year PSA at 1.0. My docs are "delighted"! My journey: