The diodes are probably there for a reason.
Do you have that diode shown on the diagram (reverse direction across motor) installed? That would supress large negative-going transients.
The diode across the motor in the diagram was one of my ideas on how to possibly reduce the inductive kickback from the motor, I do not have it installed ATM. The only diode installed in the starting diagram is the one across the relay coil. I asked if that would work so I could avoid accidentally releasing the magic smoke from some diodes if I installed them incorrectly.
Sometimes a diode is connected from the motor towards the battery + terminal. That would direct positive transients to the (low impedance) battery but not pass current when the motor is off.
Do you mean like the diagram I attached in this post?
Really think about the ground paths in a system like this. Does the battery negative cable go to the emgine as close as possible to the starter motor?
I'll admit the engine ground-to-battery cable connection is rather far away from the starter. I have a large-ish gauge wire from the battery negative going down to a bolt on the engine with all other electronics except for the head/tail/turn/dash lights and the main relay terminating their ground at the same location. That bolt is at the rear of the engine, about 10 inches from the starter motor. I'll dig around and see if I can't get a longer cable so I can ground the engine AT the starter.
Would two engine-to-battery grounding cables cause a ground-loop issue if they are both connected directly to the battery's negative terminal but to different locations on the engine?
What is the power supply for the ECU/Arduino/whatever?? Does it have good filtering / regulation from the battery supply?
What cabling is connected to the ECU and how close is it to other wiring??
The ECU is a microsquirt v2 of dubious authenticity. The power supply is on the ECU's PCB. Here's a pic (not mine) of what I'm pretty sure I am working with, minus the AMP connector:

As far as cables connected to the ECU, there are sensors (engine and air temp, barometer, throttle position pot, exhaust o2 sensor, crank trigger) and control lines (fuel pump relay, ignition, o2 sensor relay, injector, and check engine light) as well as the mandatory +12v and ground. The wires are quite close to other wires that source and sink current.
I know I need to route power wires away from signal wires as well as shield mission-critical/analog inputs, but I am attempting to run this engine with the wiring as it came when I bought it from a Chinese vendor. I am on another forum keeping a thread/journal of this project so others can know if they can buy this EFI kit and have it work with little-to-no modifications.
I am getting the distinct impression that it may run, but not well or reliably.
I read the article you linked, thank you for that! It added a few more things to tackle in this project.
Try adding an inductive choke (aka DC choke) in-line with the ECU. They tend to be good at smoothing out current spikes caused by switching.
The ECU controls and drives (well, current limits at least) the injector directly with onboard circuitry, so there is always going to be spikes of power into and out of the ECU; I don't know if adding a choke to either of those wires would help or hurt.