OK, the first two items have been addressed or are in progress. I did some more research on the third item and it appears the three '91 BBM cards were inserted in this product as buybacks, but there is no way to tell these apart from the original issue as "Topps did not specially mark, stamp, or emboss these cards" per https://baseballcardpedia.nfshost.com/index.php/1998_Bowman#1991_Japanese_BBM
If there's nothing to distinguish these, should they be listed with this set or have collection info moved and entries deleted? I think the latter and I can write up something for Trivia.
I haven't been able to find anything on the #CL4 Checklist card.