Yes, wait and see what happens. The ECU will set a code if any reading exceeds a preset limit, no matter how quickly it may come and go. Your FJR has been collecting codes for a while so they all may not be valid. Now that you have reset them, the next code to pop up will likely be a valid code.
Code 11 - No normal signal from cylinder identification sensor
Code 14 - Intake air pressure sensor hose plugged or disconnected
Code 16 - Throttle position sensor stuck.
Code 30 - Latch-up detected. No normal signal detected from lean angle sensor. (Has your FJR ever tipped on its side?)
When a sensor gives the ECU an out of range signal the ECU makes decisions based on the importance of the sensor that is out of range. The first level decision is CANNOT RUN, with a flashing check engine light or MAY OR MAY NOT RUN, depending on the code, with a solid check engine light. Next level are some codes which are UNABLE TO START/UNABLE TO RUN.
If the following codes are the result of
an ongoing out of range sensor the following actions are taken by the ECU:
Code 11 - UNABLE TO START/UNABLE TO RUN with the check engine light flashing. Since you start and can run this is a transient code that isn't ongoing.
Code 14 - ABLE TO START/ABLE TO RUN. The hose going to the intake air pressure sensor is known to plug up and a cleaning will fix it.
Code 16 - ABLE TO START/ABLE TO RUN.
Code 30 - UNABLE TO START/UNABLE TO RUN with the check engine light flashing. Since you start and can run this is a transient code that isn't ongoing.
If you have other out of range codes the ECU will ignore the sensor and operate from a fixed table stored in memory. You will almost never notice/feel an operational issue when running off of the memory table.
Your cold stalling shouldn't be caused by any of the codes you found except perhaps the throttle position sensor. In fact, if the issue causing the stalling is related to an ECU sensor it should still continue to operate normally. Implying the issue is being caused by something other than an ECU sensor.
Since you have done a lot of maintenance I will ask if your throttle stop adjustment is at the limit, either up or down. It's not critical, but the next opportunity, check the intake air pressure hose. Don't stick anything in the intake air sensor hole, and do not spray anything into the sensor opening.
The throttle position sensor has been an issue on some bikes. The sensor has a long resistor with a wiper that tracks along the resistor as the throttle is moved. It should send a 0.7 to 4.7 volt signal to the ECU from idle at 0.7 volts and wide open throttle at ~4.7 volts. As roadrunner says,
Diag. mode d01, which is showing the TPS value at idle, which should be 15-17 so it is fine.
at d01 16 = 16% of throttle opening, which is the minimum throttle plate opening needed to keep the engine idling.
Again, as roadrunner says, just check diag to see if any codes come up again. If no codes come up, the ECU isn't seeing any errors so your cold start problem is outside of the ECU Fuel Injection Control loop. This may be a clogged filter in the fuel pump, a weak fuel pump, a spark plug wire disconnected inside the plug cap (easy fix) or something else like this which is outside the FI control loop.
Edit to add: You posted while I was typing.
Sure, go ahead with the Ivan reflash.
An old RECALL should be honored by a dealer because it affects safety. A TSB (Technical Service Bulletin)
may not be honored because it isn't safety related. Some dealers will do an old TSB and others won't.
