The hc e engine has a batch fire injection system, meaning all 4 injectors fire every cycle,
It uses similar crank trigger (crank sensor) as toyotas (2 wire vrs)
The ignition timing is fully controlled by the ecu via the large ignitor. The tps and map are all similar.
If you wish to fire the engine on a 4efe ecu, then you will need to make a custom/hand made wiring harness that supports group fire injector wiring and the distributor wiring compatible with toyota too.
Your current problem is most probably due to flaky crankshaft speed sensor signal (corrupted signal to ecu) or bad ignitor (corrupted igf also does it)
Also its wise to install separate relays for main ecu and fuel pump, even the g102 charade with this engine had a large fuse box in engine room and also hanging off the positive battery terminal. Because the factory ignition switch wiring was pretty bad on daihatsu charades.