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Not that familiar with the 1.8l, but could that spare lead be for the crank angle sensor?

Could just as easily be something spurious like damage or a poor contact to the MAF sensor or the throttle position sensor. Also have you made sure you got all the engine earth straps back on and tight?

Might be worth checking the fault codes in your ECU. Do a search in miata.net to learn how.

I have a PDF version of parts of the wiring diagram for 1995 US market cars. It does not show a black/blue at the coils. However, it does show a black/blue interconnecting the O2 sensor, MAF, Coolant temp sensor, EGR posiion sensor (USA only?) and TPS. The black/blue then connects to the ECU. I'd suspect the coolant temp sensor at the back of the head (should have a black/blue wire and a blue/white wire) may be disconnected but.....

Hope this helps narrow it down.

it's pretty easy to be one tooth out on the timing belt.

well said with the camshaft teeth.....

could be anything i guess but check out this guys clips about timing belts..
http://www.youtube.com/user/MikesPlaceBiz#g/u
good step by step clip to double check timing

also when did your belt break? kms?

+1 for re-checking the belt if the plug doesn't change anything.

I've just been checking your photo against my 95 NA8. There's a lead from the coilpack wiring to the engine coolant sensor in the water connector housing just below the coilpacks. This has a plug with 2 wires, black/blue and blue/white. The plug just after the E in VALVE in your pic looks like it. If you don't have this connected then the ecu probably assumes your car is dead cold and runs fully rich.

you did not say where you were. Manga's advice sounds well worth checking. 93 may also have a very good point- you might need to recheck the alignment. Not sure if a Haynes manual can help- they did cover NA. Hope you sort it out soon.