FWIW --->
Warmed up idle speed needs to be set to 1,100 RPM.
Confirm that the 10k resistors in the plug caps are good, they sometimes oxidize and the value goes up significantly. Secondary coil resistance is 12kΩ to 18kΩ, so, putting your DMM probes in two spark plug caps (1 & 3; 2 & 4) you will get: 10kΩ + 15kΩ + 10kΩ = 35kΩ If your readings are over 100KΩ the resistors should be checked.
The fuel system should be cleaned using Yamaha Ring Free, Techron or similar product. The Ring Free will do just that, ensure the rings aren't stuck which the FJR seems prone to as well as cleaning the injectors. After using a cleaner run some straight, unadulterated fuel through the system before continuing the troubleshooting process.
Clip a DMM to the ground and signal wires of the TPS. With a stone cold engine, start it up and watch at the DMM voltage. The voltage should be stable. When the thermostat finally opens, hot coolant should flow past the wax motor on the fuel rail and the idle speed should drop and the DMM should read 0.63 to 0.72 volts and be stable.
Borrow a vacuum hose off of your sync tool for the vacuum restrictor which will stabilize the reading on a vacuum gauge or use one port of the sync tool. Put the vacuum gauge/sync tool on a sync port, start a stone cold engine and watch the intake vacuum, it should be stable, as in not wandering around or jumping. At cold idle speed, the vacuum will be lower and rise to 210 - 250 mm hg as the idle speed drops to a warm idle and should be stable at idle speed, don't sweat the actual reading, it should just be stable. Or, put the sync tool on the four sync ports of a cold engine and start it. The vacuum readings will be low due to the fuel enrichment and high idle speed. If one cylinder has notably vacuum compared to the others it may be an indication that it is much leaner than the others. Swap the injectors and see if the high reading on cold start-up follows the injector, if it does then the injector may have a clogged internal filter or may need professional cleaning.
Anyhoo, these are a few things that can be done/checked. Following these steps in order will help get a picture of what's going on. Depending on your results, they will guide the next troubleshooting steps.
Edit: I see Fred was plowing the same field as I was typing. I will note that the Gen I ECU doesn't see the O2 sensor at cold idle.