The search is on for a Second generation 43999 or 5722 Grand Seiko chronometer, box and owners manual. I have never seen a set of these, or even photos, so I have attempted to reconstruct this information from what is available on the internet.
1) Photo of first generation cal. 3180 Grand Seiko Chronometer packaging, tags and certificate:

Source: eBay auction (book)
Note that the first generation GS uses the Applique Dial 3-pointed star-inside-a-triangle logo (http://www.thewatchsite.com/index.php/topic,161.0.html) rather than the GS Lion on both the box as well as the Chronomter certificate.
2) Photo of second generation cal. 43999 Grand Seiko chronometer, receipt and owners manual (not original box)

Source: uhm, not sure, but seem to remember it was cached from Rakuten.
3) Second generation 43999 or 5722 Grand Seiko chronometer, box and owners manual

Source: cached from online sales site
So, to sum up, a complete set for the second generation GS Chronometer would appear to include:
1) Photo of first generation cal. 3180 Grand Seiko Chronometer packaging, tags and certificate:

Source: eBay auction (book)
Note that the first generation GS uses the Applique Dial 3-pointed star-inside-a-triangle logo (http://www.thewatchsite.com/index.php/topic,161.0.html) rather than the GS Lion on both the box as well as the Chronomter certificate.
2) Photo of second generation cal. 43999 Grand Seiko chronometer, receipt and owners manual (not original box)
Source: uhm, not sure, but seem to remember it was cached from Rakuten.
3) Second generation 43999 or 5722 Grand Seiko chronometer, box and owners manual

Source: cached from online sales site
So, to sum up, a complete set for the second generation GS Chronometer would appear to include:
- a black, presumable wooden box with yellow and red "Lion logo" interior as seen in figure 3,
- an owners manual as seen in figures 2 and 3
- a chronometer certificate similar to figure 1 but with Lion logo rather than the three-pointed star,
- hang-tags and price-tags similar to figure 1
- an outer protective cover in cardboard similar to figure 1
- receipt