A possible confirming method is to use a Scangage II to continuously
monitor with. This was the only way that I eventually confirmed that my
99 had an intermittent coil pack, and a bad aftermarket coil over
ignition system. P0300 is the intermittent code that is the key, along
with possible P30x codes and the P420 code. While you may need a new
cat, it's failure is likely a result of other problems. A borderline
front O2 sensor can also cause related problems. (Been there also!)
Originally, my 99 started out with undiagnosable problems involving
occasional hesitation, occasional P0420 codes, etc.
Wires and plugs were replaced several times, with subjective evidence of
some improvement. The problems eventually returned.
The Cat was replaced as part of a turbo install.
After the CAT "aged in", the occasional P0420 codes returned, and often
under an odd condition-- the next morning after frequent 500 mile
interstate runs to/from Florida. The code usually set during initial low
speed closed loop operation.
Next the 99 developed an intermittent hard to start, no start, backfire,
then maybe start symptom. Replacement of the Cam sensor seemed to have
cured this problem until it occurred again some months later. This time,
the cam and crank sensor were replaced.
To cut to the chase, I finally started continous monitoring with a
ScangageII. This showed that P0300 codes and a P0302 code were occurring
on occasion, and possibly accompanied by misfires on one or two
cylinders. Swapping parts around partially isolated this to a "Spitfire"
aftermarket coil over system, and likely the controller.
Replacement with the original coil pack showed that the aftermarket
system was at fault.
However, occasional hesitation etc. returned, and more frequent P0420 codes.
Replaced factory coil pack. Problems went away, except for a very
occasional P0420 code. If I reset it, I may go months before it sets again.
Other parts replaced, cleaned, etc during the various troubleshooting
processes
Fuel pump and filter. Used AM pump, due to turbo.
Cleaned intake manifold passages and EGR valve.
Replaced front 02 sensor, due to P0420 codes. The OEM sensor was a bit
slow to respond, and .05v low in output compared to a new sensor.
(If the rear sensor is faster than the front, a Cat efficiency code may
result.)
Also replaced Temp sensor used by the ECU.
After having the coil pack on my 95 replaced i had similar symptoms of
intermittent rough idle, so rough that i had to give it gas to keep it
from stalling, even when driving... the trusted mechanic i use was
perplexed by this and confirmed that it wasn't a ground problem (a
common problem) and knowing the cars history and solid maintenance he
could only suggest doing a fuel injector purge (plus a new set of cables
and plugs), and it worked. The car had about 125k on it at the time.
Not sure if this solution would apply to you but thought it couldn't
hurt to mention it. Let us know how it works out.
The NAs behave a bit differently than the NBs. The "no return" fuel
system is one difference, as is the coil pack on the 99-01 s.
Cam sensor failure has been a bit more common. Due to the no return fuel
system, a pressure relief valve inside the tank on some 99s was prone to
sticking partially open, causing starting problems.
I ended up replacing the OEM fuel pump, not because of any obvious
problem, but because my 99 is turbo'd and had some "raggedness" at high
power levels. This later went away when I installed a new OEM coil pack.
What was so frustrating was that the problems were very intermittent.
One thing that was misleading was that use of Techron or other strong
fuel supplements seemed to help.
The intermittent no start, rough start, backfire, and then start
normally on the next attempt really had me going for a long time.
Finally, I broke down and bought a fancy timing light that actually
worked with the miata's ignition system. This showed what looked like
random rather than timed firing, or no firing when I was able to catch
things in the act. Again, when I changed the Cam sensor, the problems
seemed to go away. In the middle of all of this, I was making 500 mile
interstate trips with little or no indications that anything was wrong.