I had a problem similar to this on my 07 125, it would miss/splutter and run very poorly in most of the mid range but would idle and run at around idle speed ok but as soon as the engine sped up it would run poorly all through the mid range up to the top end where it would start to run just ok-ish.
The problem was that one of the cdi connection was loose and dirty, so I pulled all connections, cleaned them with electrical contact cleaner, and found that one was very floppy in its fit, so squashed the female joiner so it held the pin better, taped up all the joins, this fixed the problem and never had an issue with the electrics since.
This was the last thing I did before I would have taken the bike to the shop and they would have charged me for all the checks I did myself.
It also sounds like it could be a partially blocked jet in the carb, although that wouldnt cause the timing light issue, but its just one more thing to remove from the equation.
Good luck
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