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Turns out that it doesn't matter how long you spend fiddling with it, gears will not index if you fit an 8 speed cassette by mistake to a 9 speed drivetrain. I relearn this about every 5 years, although at least it only took me a couple of hours to figure out what was wrong instead of 3 days.
Blimey! How could you think it would ever work?
Previous experiences were down to putting a new 8 speed cassette into the wrong box and just swapping a random wheel with an inflated tyre fitted instead of taking the time to fix a puncture because I was in a hurry to get to work.
This time around it was an old bike that I sorted out for a friend, late 90's Rockhopper. It arrived without wheels and with the chain rusted solid. I didn't recognize the shifters, so assumed it was old 8 speed stuff because the derailler was an ancient Acera thing. Whacked on an old 8 speed wheel and chain and took it for a ride. Shifting was about as good as you would expect given that it was thrown together with random used parts and I couldn't be arsed changing the cables which were fairly stiff. Indexing was fine at either end of the range, but hit and miss in the middle, bit like with sticky cables. I was just happy enough that it would shift, so got the brakes and other stuff sorted out, then took a look at the indexing. With hindsight, I probably should have counted the number of clicks on the shifter instead of just assuming it was 8 speed.
I spent 2 hours fiddling with a bike wondering why it wouldn't work when i'd fitted a 9 speed cassette to a bike with 8 speed shifters
it was perfect except one shift climbed two sprockets each time.
In my defence, ribble sent me the wrong cassette.....