Its a convertable, and by their very nature, the scuttle / windscreen will shake, and the car will flex way more than any tin top, so filling any join between hardtop will not work, no matter how hard you try. Sorry. (and yes i drive an MX5, with and without a hardtop, and i'm also a bodyshop technician / painter..)
The best bet is just to settle for a join and live with it.
If you look at Hilltop Automotives thread, He's actually creating a small join where the roof joins the A pillar, and that seems like great idea to me, its what i'd do too......
Sorry to bear bad news, but well done with your build and paintjob..!
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