Cherrymiata

So I have been fighting problems with my ecu for a couple days now and have literally gotten n nowhere. So let me start from the beginning; originally I had an outdated version of the MSPNP gen 2, but my dad plugged in the stn fuse which led to problems and that ecu was sent out. The ecu comes back and says rpm not synched. When you stop cranking it still thinks its cranking and eventually read 1 rpm so we ditched that ecu. So a nice new MSPNP Gen 2 later we are having problems with the injectors. First we had to synch up the timing and after we did that it was running on 3 cylinders at normal idle. Changed all the sparkplugs and still no change so we moved to injectors and checked pulse and power to injectors(power to all injectors but all cylinders had pulse except 2 and 4). This is where it gets weird; at low rpms while cranking it is obviously running on only cylinder 1 and 3 and we checked by unplugging each plug wire at a time. But it started to die and I gave it probably about 50% throttle to keep it alive and it went back to only cylinder 2 being the problem(no injector pulse when cranking but still power to injector when key on). Wiring has not changed between the old and new ecu and the tune is exactly the same. Any help is needed, my Miata has been down for over a month. (1990 NA Miata 1.6 turbo)