I did not have this problem, but I removed my control box from my
now-wrecked '96M at less than 15,000 miles. It is located underneath the
dash on the driver side, (U.S. models), and is a black plastic box that
is fairly obvious and easy to remove if you are small. You sort of have
to shove your head up under the dash to see it.

If it is fried, it probably can not be rebuilt easily or inexpensively.
I imagine that Mazda wants a decent amount of money for a new one.

I think that I still have mine, but I can't remember if I have sold it
yet. I will check my ever-growing M1 miata parts bin for it tomorrow if
you are interested in it, but like I said, I may have already sold it, I
am really losing my memory in my old age. :-)

I am parting out several miatas, and it has been a painfully slow
process that keeps getting delayed over and over. Please bear with me
Chris, Mackie, and anyone else that I have not gotten your parts off of
the car for yet.
Most of the parts will be sold on Ebay, but I have made several private
deals with people on this newsgroup for some of the parts, and they have
been satisfied.

If I have this control box, however, it is already off of the car and it
would be quick and easy to drop it in a box and mail it off to you.

If you are interested, I'll look and let you know tomorrow if I have the
alarm control box or you can e-mail me at this address privately.

Pat

I also have a '96M and had exactly the same problem - replaced the
battery after winter & fried the remote/alarm.  Even the Mazda rep I
spoke with said the security system is quite fragile (electrically).
I had the dealership replace the system (~$250) but they were close to
useless setting the sensitivity of the impact monitor or even just
connecting the sensors properly.  My impression is that the '96
security system was just a badly engineered thing.  If you really want
to keep the remote/security I would recommend a 3rd party system.
Just my 2c.
Pete