Here are a few things to consider:

Lower impedance injectors can store much more energy in them than high impedance injector of a similar inductance. Why is this information important? All of that stored energy needs to go somewhere while the injector is closed, hence the need for flyback circuitry. The flyback board, and by extension the main board, has a lot to deal with... It could also be in how the flyback board was installed (i.e. ground points, etc.).

Megasquirt only has two injector channels despite what the wiring diagrams suggest. Even though there are four pins on the connector, two pins connect to one channel and the other pins connect to the second channel.

Megasquirt does not monitor current draw or load on the injector channels. It's not "expecting" to see anything on these lines.

This configuration does not impact how you connect the injectors, nor should it impact how you connect the resistor pack. For the sake of the injector, however, you'll want one resistor for each injector (in other words, one resistor per channel will not work).

My recommendation is still the Jean's Peak and Hold (P&H) injector board. At the very least, you'll want to protect the signal from the crank angle sensor: coaxial cable with grounded sheathing is ideal, but even a twisted pair cable with one for signal and one to ground works well.

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-Paul

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