Fuel control is actually easier since you don't need exact timing, unless trying to do "sequential injection". The Megasquirt site says that isn't needed and "batch mode" is sufficient. At anything above idle, the injector sprays longer than the intake valve stays open, so timing doesn't matter. For TBI, batch mode is fine. Batch mode requires no cam sensor, only rpm, plus a few other sensors - manifold pressure, inlet temp, throttle position, or just a mass flow sensor. Injector drive is fairly simple today with a chip like the CS453 that takes TTL from the computer and can drive throttle body or multi-port injectors, high or low impedance.
Re the concern with time to charge the coil, I understand that is less a problem with an E-core coil. Look at the one on Mopar Magnum engines, GM "external coil" (85-95), or similar Ford. Otherwise, I think you must have a distributor-less system to use multiple coils.
