Update???
I have installed a lot of tops on my sale cars and other club members cars this last year. The drains have to be clean in order for the car to rid itself of water. Otherwise you are driving a bathtub.
The rain rail needs a little attention when installing it. SInce you just did a top I am thinking it isn't rivited to the top. Pull the rail again and be sure not to over bend it or it will crack. I would undo all the retainer bolts, pull the metal rails and the remove it from outside the car. I have used duct tape to fix rails and they have NOT leaked. Just make sure the tape goes on flat and to very dry surface.
Lastly, when you install the rail again, make sure the rubber flap that is under the body trim is OVER the top lip of the rear of the rain rail. You are building a path for water to go into the rail here. If you put the rain rail on top of this little rubber seal, you are giving it a path outside of the rain rail and into your trunk and interior. Looking at a cross section you should have from rear to front: body steel/rear wall of rain rain/rubber flap/top/front wall of rail rail. Good luck and keep us posted.... Chris

Sorta have an update. Im going to order a robbins rail in a few days. I havent ordered it because im about to go back to school, and Im just going to get it sent to school instead of my house. So I really havent done anything with it yet. the plus side is that it hasnt rained in awhile, so im not really having issues at the moment.

fwiw the drains were cleared a few weeks ago. and thanks for the good luck wishes.

I've been following this thread because I too have had moisture issues exactly like you described.

Last week I installed new tail-light gaskets and I think this solved my problems. For about $8 each, they were much more, "fat and soft". My old ones crumbled as I removed them and there is no way they could have been keeping a good seal.

Check yours out as a possible fix.

may also want to check the third brake light one too.

Haven't really read this whole thread but is there any chance your car was once rollbar equipped and is no longer? That'd leave room for an awful lot of water to get in if no one bothered to plug the holes.

The car still has a rollbar. Ill check the tail light gaskets as well once I get back to school.

Condensation is a problem as well for the soft tops and trunks. First clearing all of the drain holes (Do not forget the ones behind the seat on the deck panel) and getting rid of the matting, closed cell foam is a better option and still cuts noise. Then consider a good rain cover that does not itself gather moister underneath. And finally a heater fan to keep air circulating. Aside from the moister molding upholstery, the electronics will suffer too!

^Good points. My padding was wet under all of the carpet.

Your Miata has several drains:
Top of the windshield
Sides of the parcel shelf
Front and rear of the rocker panel
and probably others I have not had a need to find yet.

I learned the hard way they should be cleaned at least annually. That way you can avoid a lot of time with your shop vac sucking water out of the trunk and interior.

ok so, i also, am having the same problem as far as trunk moisture goes but i think its because i didnt seat the lid properly after repaiting but im also having leak problems over the driver side and passenger side windows. weather stripping? this can be replaced right?