You can have the timing marks line up and still have the timing off if your belt isn't installed correctly. There should be 19 belt teeth between the timing marks on the intake and exhaust cams.
Your ignition timing could also be off, which would require you check using a timing light and adjust it by rotating the CAS accordingly. Even then, you could have trouble if you have a bad crank pulley. When they age the rubber isolator ring dries and cracks and the outer pulley can slip relative to the inner portion, which would affect how your timing marks align relative to the pointer on the lower timing belt cover.
Have you verified that you followed all the steps in the tutorial correctly?
http://wiki.miata.net/tiki-index.php...ing+Belt+Steps
It's possible, although unlikely. Spark plug gap isn't super critical on a stock Miata. If you didn't measure the spark plug gap and adjust it to within spec, how would you know whether the gap was right or wrong? They don't come out of the box pre-gapped for your specific application. Sometimes they're close or even exactly what you need by mere luck of the draw. But you're supposed to always check and adjust gap if needed.
This is more likely. Too tight and you'll get whine from the excess load placed on the pulley bearing. Best fix it soon before you cause catastrophic damage to your alternator. Also, if you did not replace the timing belt idler and tensioner pulleys, or if you replaced them with poor quality aftermarket items, you can get noise from those bearings also.