The control box for the 280ZX injection is not as sophisticated as other models later in the series - no safety mode, no diagnostics. In fact in the UK versions, no main ROM!
The cold temperature starting depends on:
1. The ECU water temp sensor value which determines the firing rate for the injectors.
2. The thermotime switch which determines whether the seventh "cold start" injector should be firing.
3. The throttle by-pass or air regulator valve which allows extra air past the throttle body to compensate for the additional fuelling provided by the other two systems. Valve is open when cold and gradually shut down by a bimetallic strip heated electrically and a pad of warm / hot water on the underside (the reason for the little water hoses on the intake manifold).
A change in running between hot and cold will be accounted for by faults in one, or a combination, of these devices.
Air flow is determined by the the AFM - a fairly crude flap device which regularly plays up on the 280ZX and may cause rough running, poor transition from idle or just plain old failure. Don't be tempted to play with the shrouded adjustment (air by-pass) screw unless you fully understand what you are doing!
Re. alternator - have you checked that the new alternator is giving a suitable voltage to the battery. The ECU is voltage dependent and if it drops below 12V it will cause poor running and eventually failure...
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