G'day. So what you are saying is;
1. That you have a hardtop on your 5
2. Water is leaking in around the rear of the soft top
3. Soft top is going moldy
4. Set plates (3 metal plates holding soft top tight) are rusting.
It may not be the frankenstien bolt that is causing the water incursion issue. The MX-5 has a 'rain rail' that runs around the lower back edge of the soft top. The job of the rail is to capture any water falling on the roof/rear of the car and divert to two drain holes/tubes on either side of the cockpit. If the rain rail becomes damaged it can cause the issue you have described. Also, if the two drain holes/tubes become blocked with dirt or leaves then the water can flow back into the cabin and wet the soft top and back tray.
First thing is to check/clean the two drain holes/tubes. If you do a search on this forum you should find a few recent threads on how to do that.
Next I would get the car into a dry place, remove the hard top, put the soft top up and allow it to dry out. You may need to make up a mild cleaning solution to help remove any stains from the soft top.
With the roof up I would look at the rear of the cockpit and see how damp the carpet is, and check if you can see where the water is coming in. You may have to remove the rain rail to repair or replace it. It may look like a challenge, but nothing you can't do with the right tools and common sense.
There is some great info, including photos on the US form covering these very topics.
http://www.miata.net/garage/garagetops.htmlJ