I know nothing about the honda engine or your ECU. However, if I knew my ECU was 10* off, my first thought would be that the loss of performance was due to ignition timing being off, rather than injector timing.
Most MS'ed miatas run batch injection. Two banks of two injectors, and each bank squirts twice per engine cycle. I don't have tunerstudio on this computer so I can't look at the menus or default settings right now, but with MS2 and MS3 you can run sequential and you can control the squirt timing. MS1 didn't have that capability.
In my reading on setting up sequential fuel I came across some info on the jbperf website (JB makes expansion boards for MS) that covers the settings in MS. Don't know if that would be of any use to you, but here it is
. One thing you can glean from that is the injector timing is usually held fixed, whereas spark timing is dynamic. So if you are asking if the injectors fire at the same time as the spark plugs, the answer would probably be no, or at least "not always." If you merely adjusted your spark map 10* to account for the sensor placement, that probably didn't fix your injection timing.
It sounds to me like you should just sync up your ECU to the motor and that would fix both, assuming your ECU controls both fuel and spark. For example with MS we tell the ECU to give a fixed 10* ignition timing, then using a timing light we adjust the trigger offset in the software such that there is actually 10* at the crank. Your sensor/tooth discrepancy wouldn't matter if the offset could be adjusted by your ECU to sync it up with the motor.
The only discussion I recall seeing here about injection timing was from the few people running sequential injection. Maybe one of them will pipe up with some more useful info. Most of us are running batch and haven't messed with it.