Shimano Sora 9-speed shifters "missing a speed" First time posting, hope I can get some suggestions on this weird issue I've noticed with my shifting. I have a fairly decent understanding of how to maintain gears myself, and have made quite a few attempts at trouble shooting this, so unless I've missed something it seems to be something beyond the obvious 'reindex, replace cable-housing, lube chain' sort of thing. 

The Problem
So basically, my 9-speed shifters which are a few years old, seem to only click through 8 speeds, both ways. This manifests in the chain always 'skipping' a cog on the 9-speed cassette no matter how I index, although I think the cog it skips varies depending on whether I'm shifting up or down.

Notes


I have recently replaced the chain, the cassette, the cables (lubed) AND the housing, so I am fairly certain it is none of these.
The deraileur seems to be indexed correctly: transmission is quick and crisp and and both extermes of the cassette can be reached when shifting through all the speeds.
I have come off the bike on the the derailleur side before, but the fact both extremes can be reached seems to suggest a bent mount isn't the problem?
The shifter seems to physically only click through 8 speeds, despite most definitely being 9 speed.
Chain is 9 speed


For all I know it could be a common problem, but not one I'm familiar with. Is there some sort of adjustment needed on the shifters themselves? 

Any informed suggestions greatly appearciated! 

Thanks
I'm kind of confused here. You say you can only click 8 times. On a 9 speed bike, there would only be 8 clicks for shifting.  Let's say you start on the largest gear, and we'll call that 1.  Clicking 1 time with bring you to gear 2. Clicking 2 times will bring you to 3. Clicking 3 times with bring you to 4. Continuing on with the pattern will bring you on to clicking 8 times to bring you to 9.  

If you bike was skipping a gear somewhere in the middle, you would shift 7 times, and already be on the smallest gear, and shifting one more time would bring you nowhere, as you would already be at the bottom. The limit screw would keep it in it's place, and the cable would go a bit slack. Going up the cassette you would notice a problem where you still had 1 click left, but would be unable to move the shifter because you would be pushing against the limit screw.