Sounds like you are making progress
When it does start up, there does seem to be a kind of knocking noise from the engine.
Normal for a motor running on only 2 cylinders
Both coils are new and primary readings are 3.6 ohm. The secondary readings are 16 kohm, with the caps on 27 ohm.
Stock coils have lower primary resistance .
I have no idea what impact your 3.6 ohm coils may have on other components of your ignition system
Having said that you could try the following
Pull all 4 spark plugs and ground them on the engine while connected to their plug caps and plug wires. Hit the starter button. Have you spark on all 4 plugs including the 1 - 4 plugs ?
If yes then problem is valves compression or fuel/carbs.
If still no spark on 1-4 plugs then swap the black and green wires to the other coil. It does not matter if you swap the red wires to the other coil as these both carry battery voltage all the time ignition is on. it does matter which coil the green is connected to and which coil te blackis connected to. I just cant remember if green is for 1-4 and black is for 2-3 or vice versa.
In swapping wires you are trying to see if the problem follows the wires.
With black and green swapped hit the starter button again. Did the problem follow the colored wire to the 1 - 4 coil?
If no then problem is with plugs, plug caps, coil etc.
If yes then trace back that colored wire - Is there continuity (ohms) from wire at coil to connector at ignitor? Is there continuity from ignitor to the pick-up coil under the CD sized cover on the right hand end of the crank?
Crack open the manual and follow tests for ignitor and pick-up coil
Good luck
PS dont forget to swap back the coil wires to where they should be