you mention 'clutch' so I am assuming that you have a manual transmission. And now, I am confused by the question.

"If I am sitting at a stop sign or a light and keep one foot on the clutch and then give it gas when I start, the car does ok."

Isn't that the normal way to get get the car moving? I presume that you meant start moving when you said start, and not start the engine. I am also assuming that you also begin to let out the clutch to get the car in motion.

Now comes the part I am wonder about:
" But if I just press the gas, it sputters and jerks."

Is the clutch fully depressed, or did you suddently fully release the clutch (causing the engine to sputter and jerk)?

Or maybe the transmission was put into neutral, the clutch let out and then it misses when the throttle is depressed.

Another thought along a different track: Does your car have an interlock on the clutch, i.e., the clutch must be depressed to engage the starter. I would think that such an interlock merely prevents the starter motor from being energized, and does not affect the ignition. But if such an interlock also kills the ignition, that part may not be functioning properly. [you can tell by now that I have no information about the Miata, but am guessing.]

Let us know what you find.

Do you know about miata.net?

Yes I have heard of miata.net, but I was looking for more general stuff I guess. The more I drive it, the more I think it's fuel related and not emission related. I have put this issue on hold since we're going on vacation in a different car for a while.

"As I release the clutch and depress the gas"=start moving I have never sudden or fully released the clutch, that would cause it to stall, even with it in perfect condition ;) However, you hit the nail on the head... the part I too am puzzled about... with the gas depressed only, with the clutch to its final destination, that's when it sputters. If I hold the clutch and the gas to continue forward, it doesn't sputter. That's why I think it's fuel related. I'll just keep filling up with the best fuel+an additive. That seemed to help quit a bit. Until I get it looked at professionally.

Until then, any other thoughts?