My long day-into-night randonneur rides mean I often include a wearable LED headlight in my kit so I can effect repairs in what otherwise would be moonlight or dark of night.

After one 02:00 puncture where I spent more time looking for my presta valve cap than I did repairing the puncture, I wrapped a thin strip of self-adhesive reflective tape around each cap and never had to hunt again as they showed brightly in the sweep of my light. Did the same for my black tire levers and put an additional spot on my patch kit.

Sure made life easier!

Best, Dan.

How much motor traffic did you meet on those roads, and how courteous were the drivers?

Once I was away from the larger urban areas, I was mostly able to plot a course that avoided the busier roads. There are a lot of roads to choose from. Sometimes it was a balancing act, because getting off the main highway meant meandering through a maze of back alleys with stop signs every block, or climbing a hundred meters up a 20% slope to avoid the highway following the river valley. A lot of times though, even on the main road there would only be a one car passing every couple of minutes. I would say in 26 days of riding there were only about 30km where I thought to myself “this sucks”. 

The level of courtesy shown by Japanese drivers is almost incomprehensible to someone coming from North America. On the few occasions that my route planning was less than stellar and I found myself on the side of a busy, shoulderless highway, I was never passed “too close for comfort”. Most cars were small enough to pass without crossing the centre line, although most moved over when possible. Every one of the trucks would wait patiently for a break in oncoming traffic to give me a wide berth, even when I was grinding uphill at 6km/h. Leaving Kagoshima, on a particularly busy stretch, trucks would be stuck behind me for a minute or more before there was a break, or I could find a place to pull off and let them pass. No horns, no crowding, no drama, just patiently waiting. I always gave them a thank you wave, which was always returned with a friendly tap of the horn.

Japan also has a 60km/h highway speed limit everywhere but on limited access expressways where bikes are forbidden. Even though this seems to be a “guideline” rather than a rule, it meant even on highways most vehicles were going 70ish, compared to here in Canada and USA where everyone on two lane highways passes at 100 to 120 without slowing down or moving over.

I'm sticking with 700C for now.
I like mudguards, but I also like riding on muddy trails.
As you say, the two don't always mix well.
I may try some 'gravel' guards and see if that works as a compromise.

I now have a new Mk3 Mercury frame & fork as a replacement for my damaged Mk2 frame.

Sounds like a good decision if you were already happy with the damaged one.  Are you sticking with 700c?  The extra frame clearance comes from dropping the ability to take a caliper brake, which also allowed for the full sized EBB.  I have a 40mm Schwalbe Efficiency on the back, their replacement for the Supreme, a bit chunkier though Schwalbe claim - "Our fasted ever touring tyre" There's adequate clearance under the 55mm guards, though they can collect enough mud to rub on mucky lanes.
I have the 700c only 853 fork, same as I had on my previous Mercury, there's a 40mm Supreme in that with adequate clearance, though those measure closer to 38mm on my rims. 
Black fork on the gray frame look neat together IMO, I had a black touring fork in mine at one time.

Agreed. I grip them between my teeth to save losing them in the grass/dirt.