
So I read Love is an Illusion first and the main couple there is the same but the storyline's totally different. Did the author decide to use the same characters but changed the story? Thanks in advance if you can enlighten me!

Its like theyre in another universe...
And theres a glimpse of the 1st couple: http://www.mangago.zone/read-manga/love_is_an_illusion/uu/love_is_an_illusion-chapter-20/5/

When Shunsuke is already a working adult and helps Aki with the shop's accounting. I just can't for the life of me remember where I've read it!

I think you mean another manga, because I remember there's one that has similar plotline, a part timer falling for his boss and it ends up like you described. The boss is divorced though (or lived together with his girlfriend until she suddenly disappeared). Since he worked there every summer for years, he knows it all.

Finally find it after a long search (⌒▽⌒)
http://www.mangago.zone/read-manga/umi_to_futari_no_enbun_noudo/
Of Akiyama x Sato They're such good kids!