The method I use is to simply kill the system, then setup a vertical blank interrupt handler that counts frames. The main code then executes the test code a million times (for PAL). On a 50 mhz CPU this will give you the time in cycles (don't forget the loop overhead). Works for single instructions.
For different clock speeds and refresh rates just calculate a different number of times the test code has to be executed. Example: PAL+25 mhz CPU=500000 times.
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