I got the water pump cover off, and removed the front crankcase cover. The impeller was pressed out using a hydraulic press, according to the manual, and the impeller ball bearing was removed with a bearing puller and slide hammer (after heating the bearing seating area. The mechanical seal was removed using the hydraulic press, so I'm down to reassembling the new parts.
Using the shop manual and parts fische, observing where things were prior to disassembly, and checking what fits where, I've established where everything but one part goes. There's a small seal that appears to fit underneath the impeller ball bearing on the back side of the crankcase cover. Nothing else fits the small depression in the casting that houses the bearing. I assume that the old seal popped out when the bearing was pulled, but we haven't found it. This seal is #9 (oil seal) on the parts fische:
http://www.bikebandit.com/oem-parts/2005-honda-st1300-st1300/o/m2528#sch409983
This seal is solid on one side, and has a groove (with a tensioning spring) on the other side. I don't know which direction the groove faces. If it's there to keep crankcase oil from flowing forward into the pump on the front side of the crankcase cover, I would assume that the groove should face rearward towards where the engine oil is.
Any guidance from those who've done this job, or who have a better understanding of seal placement than I?
Clicking on the photos should make them a bit clearer.