Your MX5 will be the Mk.3? I have a MK3.5 which is similar and has improved hood drainage which was bad on the Mk 2.5. So firstly check the reason for the rot which may well be related to hood drainage. I had a mk2.5 previously and drenched the inside of the sills with Dinitrol. However you do have to keep the drainage holes under the sills clear. After a hot summer the Dinitrol melted and blocked up the drainage holes. The sills eventually filled with water and started to rot!
The MK3 and 3.5 are nice everyday practical fun sports cars (especially the 2 litre). Nothing to compare really (apart from the Honda S2000). Probably worth keeping hold of and getting the work done. Having said that I'm selling mine this spring and using the Morgan if I need a car when the wife's car isn't available.
Good luck with whatever you decide to do.
