Both Javascript and Flash are definitely the wrong tools for the job if you need high precision timing for research, because of something nobody's mentioned yet: garbage collection pauses. Every few seconds or minutes they will pause everything and go and clean up memory, and this can take 10 - 1000ms. A 100ms pause isn't uncommon and it essentially be happening randomly, whenever the memory usage conditions become suitable for collection. So if you are making high precision time measurements, you will basically get random delays added in to your results, and not all of them will even be noticable.
You could use Construct Classic, but it is still a step-based game engine and not really designed for high accuracy measurements. For example, it uses double-buffering, meaning there is another one frame latency before visual feedback appears on the screen, and in some circumstances it may even use triple buffering.
Computers are capable of microsecond precision in their timers, which might be supported in Javascript depending on the browser, and is supported in Construct Classic. However, I've heard that PC input is sampled for the mouse, so mouse input will only update at 50-100 Hz, so if you are using mouse input your results will only be coming in at 10-20ms increments anyway. I don't know about keyboard input though.
TBH I don't know much about extreme precision measurements on PC - we make game engines which generally are designed to smooth out inaccuracies over time and are optimise to look good rather than be perfectly accurate. I'd recommend getting specialist advice and tools, I don't think any of us can give you the necessary information you need.