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my guess is its not electric shifted, (what trans model is it)
so step 2 in the FSM book says.... and i paraphrase
step1 is stall test (my guess passes in 1st and reverse)
step 2, line pressure test?
if that fails, tranny is bad.
The governor gear may have stripped,it's plactic. Just in front of the tailshaft there is a round cover about 4 inches around, some have a wire clip over the cover. Pop the cover off,(might lose about 1/2 cup of fluid) Pull the governor out (should be very easy) If the plastic gear on the end is "apple cored" or at all damaged , it will keep the ****** in low.As will having no vacuum to the modulator valve.
the yzf600r has a large gap between 1st and 2nd gear. if you don't shift into second firmly every time, what happens it that over time the dogs which engage 2nd gear gets worn/rounded off, and the "falling out" starts to occur during hard acceleration in 2nd. once the problem is there, the only way to fix it is to replace the affected gears: 2nd and 6th ( the gear 2nd slides in to), the shift fork, and the shift cam.
this requires a complete teardown and splitting the cases. about $3-400 in parts, depending on where you purchase them, and 8-12 hours labor depending on your level of expertise.
If it's a later model (post 98), then I have an idea what's happened. On the rounded ball end of the gear stick that goes in the box, there is meant to be a plastic bush that is only a very loose fit on the end of the stick. If it has dropped while either removing or replacing the gearstick, and fallen into the area at the back of where the gearstick actuates the shift rail, then apart from having a very sloppy gearstick, you won't be able to move the shift rail backwards - which is what happens when you move the gearstick forward (1st,3rd,5th). This should be fixable from in the cab. Of course, if you have an earlier model, none of the above applies, as you have the gearstick moving only one of a choice of three shift rails with no bush in that area. The only thing that happens to those is the spring on the gearstick breaks (that can't be replaced on its own!)
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