I bought a USB cigarette lighter adapter with a digital volt meter on it. It reads about 1/2 volt higher than my dash gauge. I check it every so often to make sure my system is working OK.
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All you've done by only testing the battery voltage is confirm that with the current load, the alternator and the battery are not the issue. This doesn't mean they aren't an issue (more on that in a second). Your primary concern is hyper flash, and low voltage to components that are not directly connected to the battery, this is why it is important to test resistance from positive terminal to main power feed for these circuits. It's also possible that there is some resistance between the negative terminal and the ground that these components are connected to, hence the need to test resistance between negative terminal and main ground points (frame, body, engine). Even if all of this checks out, your lights may flash at varying frequencies due to the fact that you are using resistors to trick the flasher relay into performing them at the same rate that a light bulb would. The problem with this is that resistors act differently with heat than light bulbs do. Resistance increases as temperature goes up, light bulb filaments tend to reach operating temperature very quickly and cool off relatively quickly as well, whereas a ceramic resistor is going to heat up more slowly, but retain heat for longer. This is a reason that people will recommend using a flasher relay designed to operate with LEDs, rather than an inline resistor setup (I recall a few posts from TheAutumnWind on this exact topic IIRC). All that being said, you still have more testing to do to ensure that your components are receiving adequate voltage, but even if they are, you may still experience hyper flash due to the fact that resistors are not the same as light bulbs and will have a different effect on the load of the system while in operation, even if they're rated at the same resistance when combined with the LED as the stock bulb. In order to completely alleviate the issue, you need to fully test your electrical system to first ensure that everything is getting the proper voltage, then if you're still having issues, it's probably due to the resistors either being out of spec, or reacting differently under load than the flasher relay is expecting it to, causing the frequency to vary.
Now, regarding the alternator and battery. While it may test in spec now, if you find that you're not getting good power connectivity, or ground connectivity to these circuits, you may find your alternator and battery with a higher load once you've cleared the issue. If you find and fix issues regarding power or ground connectivity, retest the system with all possible loads you can put on the system while idling. If your system voltage drops below 14V during this stress test, you need more power. Rev engine to 2000 RPM and repeat test. If it's able to maintain 14V or more at 2k, you need an alternator that puts out 140A at idle, not peak. If it drops below 14V at 2k, you need a much higher rated alternator to maintain voltage at idle.