I'm trying to get the K (1990 16v) up and running after an engine replacement. I've set the bike up on the table removed the timing cover set the pickup in spark plug 1 and used an independent battery. Warming up the bike I proceeded to remove the two mud-guards and the pick up cover and just waited 5 minutes to make sure most things are warm. 

Set the timing light to 6deg and set the cylinder to 4. loosened off the locking screws and watched the two notches.
First test, the notch was below the set one so made the adjustment and it aligned nicely.
While holding the strobe I turned the throttle and the marks moved away again, made a change and around 2500rpm they looked near in synch. 
Went to 3000-3500rmp the strobe light turns off the bike sounds like its popping and I cant see the notches as the strobe light out.

Could this be a coil issue or a spark plug issue as both have been replaced?

Drop RMP and the light turns back on and the bike sounds ok-ish

Although I'd be satisfied with the method described in the K1/K100RS 4V manual, I found this article that could have a bearing on your situation regarding your technique with the timing light.

Thanks for this. I’ll check this out tomorrow

What is wrong with just lining up the notches in the HES plates?  Thousands of bricks have been running with that timing for 30+ years and hundreds of millions of miles.   Asking for a friend.

+1 there you do no need to use a timing light as the marks are TDC not ignition firing point. There are many threads here about the correct wat and a strobe is not needed. Aligning the two notches will get it to within 1° every time. I have never done it any other way and never had problems.

All good replies. Thanks all and I will start the search of how to.....Right now I'll try the alignment of the notches and see how it feels.