I find it a little strange that your resistance measurements have that much of a difference between the pickup connector and at the ecm connector. granted, the 518 ohms is still within spec, but you shouldn't see a 50 ohm difference between those 2 points. double check you are getting a good connection when you plug the pickup coil into the main harness. you may have to ohm out between the main harness side of the pickup coil to the main harness side of the ecm connector to see if maybe you have a wire showing signs of breaking. you should only see a few ohms between those 2 points.

 

Testing Update for Oct. 9, 2023:
Pulse coil resistance check from Y and Y+W wires - 455 ohms at ECU multiport connector. (Wire color yellow and yellow with wide white stripe)
Pulse coil resistance check from Y and W+W wires - 454 ohms at red plastic plug wire connector right off the coil.
Following the directions of the new coil supplier stating that if the engine does not run properly, swap the Y and W wires from the coil to the red wire connector. I did swap the wires and the engine started and ran but poorly. The engine backfired when started and needed extra help from the starter to get into idle. The engine runs in idle but is very hesitant to stay running. When throttle position is increased there was delay in RPM and hesitation. So swap of the wires offered no improvement so I will return the wires so yellow and white wires off the new coil connect to yellow and yellow and wide white stripe wires of the wiring harness.
The next action I plan to take is to reduce the coil gap from the pick-up rotor spokes. Coil supplier states coil gap should be close to 0.010" and I measure 0.018" of coil gap. By design, there is no adjustment in the installation that is easy. The coil installs the same as the OEM coil and "self-centers" on the support prongs of the right side engine cover.
I plan on removing the cover again and set up a dial indicator within the cover to measure the existing location of the coil face. I will remove the coil, and use a Demel rotary tool to slightly open up the coil frame mounting holes then install the coil reducing the gap to the pulse rotor spokes. Once the right side cover is installed again, I will check the gap using brass feeler blades again to confirm I have reached my gap target.
If I had a peak voltage adapter for my meter, I would be able to confirm pre-gap change voltage from the coil and after gap change improvement of voltage. I currently do not have the voltage adapter.
I hope it is the pulse coil gap issue that is causing the poor engine performance.

 

You've got extra resistance in pick-up coils wiring between coils and ECU. That may attenuate already weak signal from pickups. Disassemble connectors and clean terminals with contact cleaner. Also pinch female terminals so they have tighter bite. Then re-measure impedance of coils at ECU connector. Should be exactly same as measuring at sensors themselves.

 

Mine measures 491 ohms and runs fine?

 

Testing update Oct. 21, 2023:
Performed electrical contact cleaning of the coil wire connections using electrical cleaner that is safe for plastic contact.
Resistance at red plastic plug of the pulse coil wires = 453.6 ohms. Test #2 453.6 ohms. Test #3 453.6 ohms.
Resistance at ECU multiport plug for coil wires Y, Y+W = 453.6 ohms. Test #2 453.6 ohms.
Battery at rest = 13.06 VDC
Started engine instantly on first push of starter button. Idles, but does not sound heathy and strong and is very sensitive to stalling. Alternator charges battery while idling at 14.43 volts.
Interesting finding - Engine will stall if front brake lever is pulled in. Engine will stall if back brake pedal is pushed down. Engine chugs when turn signal is on in unison with the flash.
So minor changes in system voltage negatively impact engine operation causing it to stall.
I monitored my multimeter connected to my battery during these tests and charge voltage remained just above 14 volts, and when brake lever pulled in, engine stalls then charge voltage drops when engine stops.
There is a very sensitive electrical problem that needs to be corrected.
What checks should be performed to find the cause of this problem?
Thanks

 

Inspect the integrity of your ground connection. Do a continuity test between the negative terminal of your batter to the frame. You should see low ohms. You might need to clean the ground connection on both sides of the negative terminal.

 

Ground connection check - Took the ground wire off the battery terminal to clean the the connection and found the terminal bolt not as tight as it should have been. Used some fine sandpaper to clean both sides of the connecting lug and the top of the battery terminal then assembled and performed a continuity test with the result of 0.2 ohms from negative lug to seat frame.
Removed and cleaned the positive lug as well.
Started the engine and the system power change problem still exists. The engine runs in idle but when power is used for brake lights, the engine will stall. The slight drop in system power impacts the engine.
Overall the engine does not sound healthy. It sounds "crackly" and not smooth. Before this problem, backfiring would maybe happen once per year and I ride often. Now the engine could backfire once during my testing on a daily short use of operation.

 

Its almost sounding like a failed CDI box, but I can't imagine that would cause the the engine to die when the brake is applied and putting a draw on the electrical system. This may seem odd, but remove the bulbs from the brake lights, start the engine and apply the brake again. Im wondering if you have a dead short in the brake lights causing a dead short. The only counter thought to that is that the fuse should have blown if that was the case.

 

Also clean ground connections on frame. Follow battery ground cable and clean it where it bolts to engine. There may also be additional ground cable connecting engine to frame. Disconnect both ends of this cable and clean.

Then find cluster of ground cables at front left of frame and disassemble them there for cleaning as well. Slobber dielectric grease over joint after it's reconnected to keep moisture and corrosion out.

1. measure battery voltage with bike running, volts =???
2. keep probes on battery and step on brakes, volts = ???

3. measure voltage at ECU blk/wht power wire with bike running, volts = ???
4. keep probe on ECU blk/wht power wire and step on brakes, volts = ???

There's something wrong with wiring. By getting numbers at different locations, we can track down where problem is.

 

Test results for Oct. 23, 2023:
I took both brake light bulbs out, started the engine and applied the brakes, front then back and there was no change in the idle running condition.
Using the turn signal does impact the engine operation causing the engine to "flutter" in unison with the flashing lights but the power draw is not enough to cause a stall.
Turning on the high-beam headlight also did not stall the engine.
If I only put in one brake light and apply the brakes, the engine continues to idle. Two brake lights installed will cause a stall when the brakes are applied.
Ground connection cleaning -
Followed the main ground from the negative of the battery and it is connected to the engine case at the back of the starter support. The ground cable lug bolt is hidden under a coolant hose in a horrible location that I was unable to get a wrench on. I tried stubby wrenches, long thin wrenches, s-shaped obstruction wrenches and due to the location, I could not get a turn on the bolt head. I tilted my fuel tank and tried to come down to the bolt with a socket from above but with the coolant hose in the way I could not get on the bolt. My crows-foot set did not have the right size and that may have worked. So to continue testing, I made up and installed a second temporary ground cable from the top of the battery to the seat support frame.
The wiring harness ground was easy to access under the fuel tank so it was unfastened and cleaned up with fine sandpaper and Scotch-brite pad.
Started the engine and no improvement to the electrical system.
1. measure battery voltage with bike running, volts = 14.60 volts
2. keep probes on battery and step on brakes, volts = Engine stalls when brakes applied and both brake bulbs work. Voltage on battery is 14.43 volts fluctuating to 14.60 volts (unchanged) when both brake bulbs are removed. When turn signals are used the battery voltage dips to 13.8 volts.

3. measure voltage at ECU blk/wht power wire with bike running, volts = 13.82 volts
4. keep probe on ECU blk/wht power wire and step on brakes, volts = 13.82 volts with brake light bulbs removed, front brake lever pulled in. Doing this test with brake lights installed causes stall.
Doing this test with only one brake light bulb installed causes a small reduction in power = 13.74 volts.

I keep thinking about the new pulse generator coil that was installed could possibly be part of the cause of these ongoing problems. Yes the engine now starts and will idle, but it does not run well. The gap of the coil pick-up face to the spoke of the pulse rotor is out of tolerance. The gap should be 0.010 inches and it is 0.018 inches. Options are to try to adjust the new coil position or purchase another new coil of a different brand. I may just order a new coil in hopes that will result in improvements. I could also order a peak-voltage adapter to obtain the voltage from my coil and see if it in fact performs to targets the Honda manual states.