I didn't use any sealant on the new seals but I made sure they were in place when I got the valve cover pushed back on. I also didn't replace the dowel pins since they seemed to be press-fit in place and there wasn't anything wrong with them. I cleaned and tightened the spark plug wire connections at the plugs and the coils while I was in there. I took the bike out for a run and it gets up and goes just fine.
I noticed the bike was missing the coolant reservoir cover on the bottom fairing in front. I thought I might have forgot to reinstall it last time - but I think what happened is that it vibrated loose because I didn't tighten the two screws that hold it in place. I am fabricating a cover using some scrap plastic, fiberglass mesh and ABS glue. A new OEM cover is 30 or 40 bucks...so I'll see if my homemade one does the job.
It's amazing how much time I can spend fiddling around with this bike - but I'm learning and it's better than watching TV, mindlessly eating or aimlessly surfing the web. I didn't refer to any instructions or manuals today other than to check the torque values for some of the critical bolts. I spent a quite a bit of time fitting screws back into the fairings and side pockets. Using the screw map that came with Murph's screw kit will be a big time saver.
I still want to repair the crack in the upper fairing, install the Murph screw kit, and install the knee savers peg lowering kit when that arrives. I was thinking about replacing the spliced main fuel line - had my hemostats ready - but I decided against it since I put in a full day anyway and can image it could take a lot of futzing to get the new line on the carb bank and I'm not sure about ever getting a clamp on that line given the access. The splice I put in there is working fine.
Right now the bike is good to go and I hope to take it for a ride tomorrow after I install the coolant reservoir cover and make sure those screws are good and tight.