I saw this in a Tokyo theater in '99. "Mothra 3" is easily the best of the 1990's Mothra films, though it still falls short of Toho's classics. It features the return of King Ghidorah (the huge, three-headed flying cosmic dragon, not the underwhelming, four-footed "Death Ghidorah" of the 1997 film)... after Mothra fails to defeat Ghidorah in the modern day, she time-travels back to the Cretaceous, where King Ghidorah (millions of years younger, of course, and slightly less powerful) is busy wiping out the dinosaurs, and she tries to defeat him there.
The tiny Mothra and tiny dragon that Scott remembers were also in this film (and in the 1997 and 1998 films), but they're not the focus.
Highlights include an all-too-brief onslaught against a modern Japanese city by Ghidorah, who looks more powerful and evil in this film than ever before.
Here's the poster (coincidentally, I just bought one of these on eBay, last month)...
As far as I know, this hasn't been released on American DVD. It's a shame, because it's worth it for the Ghidorah footage alone.