You can adjust the catches at the top of the windscreen, but I don’t think they will make a huge difference to the position of the hardtop. I think there is some method of adjusting the clips that go over the Frankenstien bolts, but I don’t know how. Mine just fitted straight on.
The full hardtop fitting instructions used to be on mx-5.com, but no more. Anyway:
Get the rear deck adjustment right. Undo the little grub screws and open the chrome covers (they’re hinged at the corner). Undo the two bolts (12mm, I think) holding each clamp plate in position.
Slide the hardtop forward until there is an even gap of about 3-5mm between the front of the top and the header rail. Don’t fasten the front catches.
Tighten the rear bolts to fix the adjustment.
Now adjust the front latches as for the soft top, using the hex adjuster under tha plastic cover. They should take a moderate push to close, and the gap should still be even when they are closed.
When you’re happy, adjust the middle latches in the same way.
Finally, close the rear deck latch covers and tighten the grub screws.
A few tips: apply plumber’s liquid silicone to the long seal where the top meets the car body and to the gaskets of the rear deck latches - it helps the hardtop slide into position without the seal rucking up. The gaskets get torn easily and can be ordered as spares from a Mazda dealer. To form a good water seal the latches don’t have to be mega-tight, but they should be evenly tight all round. If the top looks high in the middle of the header rail, move the front latches outward (using their three retaining screws*) to pull it tight.
*these are easily rounded out; I had to drill one out - ruined by a previous owner - and then use molegrips on the shank. I replaced with Torx screws.