Miata running roughly upon start up? Maybe even running on 2 or 0 cylinders? This is most likely your ignition coil going/gone bad. This is a job anyone willing to learn can accomplish in under an hour (typically). The process is about the same for NA and NB models (My car is a ‘96).
“Except 01 and newer switched to coil on plug i believe.” (quote from thedok) -thanks!
Tools: OEM Ignition Coil, 10mm and 12mm socket/wrench, flat head screw driver, pliers, and towel/rag (for all the blood and engine grease).
Here’s my new OEM Ignition Coil:
First step is to disconnect the negative battery terminal using the 10mm ratchet/wrench and discharge the residual power by pressing in on the brakes.
Secondly remove the existing ignition coil. Start by undoing the spark plug wires (be sure you remember their order) and unclipping 3 clips that connect a few pesky wires, which will be in your way. 1 of the clips is on the passenger side and 2 are on the driver side. I also moved the black wire that was clipped to the metal wire, which you can see in the top left in the picture below. Anything else that may be in your way; remove/move out of the way as needed.
Note: There is also a snap in thingy you will have to undo, that holds the wrapped wires going across the top of the ignition coil in place. Use the pliers to release this.
The ignition coil itself is held on by 3 12mm bolts: the top 2 are easily visible, but a little tricky to get to. The third bolt is not at all visible and more difficult to access. What I did, was reach back there with my bare hand to feel for where exactly it is. Once found, standing on the passenger side (USDM) reach in with your right hand holding a 12mm ratchet (or wrench if that works better for you). This will not be easy, but can be done. Undo all bolts with care, as dropping a bolt or ratchet/wrench could be pretty bad depending on where it goes.
Note: Using a flat head screw driver will help with prying the clips off.
Once the bolts are all off you can move the ignition coil somewhat freely, until you find a way to access the two (in my case) clips on the coil itself. Unclip both of these, being sure not to damage them. Then remove coil (may be a little tricky, but it is possible).
Now you can install the new coil! From what I hear, most people only bolt the top 2 bolts back on with no ill effects. I actually did all 3... well almost. My third bolt is mostly on, but I just can’t tighten it anymore, so I might back it out and try yet again, to get it on all the way (maybe it’s crossthreaded? Idk).
Note: If you decide to use the third bolt, you will need to reuse the washer and rubber surround from the old coil. First remove the center washer and then you’ll need to persuade the rubber surround out using ingenuity.
Good luck to all of you and thanks for reading! You will most likely skin a few of your knuckles in this process. Embrace it; these are the battle scars of men (and women too)!
Original article I referenced before attempting this for the first time: