Forks raised in the yokes by 25mm is a lot and very unlikely to have been done without the rear being lowered too. Measure the hole centres on the linkage bones. I seem to remember that 128mm is standard, certainly if they are longer than 130mm your bike has been lowered at the back too.

Fitting a fueling device to richen the mixture will help a lot with the bogging down at lower revs, it did with mine anyway, which will now pull smoothly from 2500rpm rather than nearer to 3500rpm before.

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