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So long story but..
Saw some wear in my outer cable so decided to replace it last night, new outer is the same length and routing as the old. Put new inner in at the same time and connected it all back up. Gears were working alright before I started, not perfect but liveable.
After connecting it all back up I checked the limits and the b tension. All fine as I haven’t actually touched anything other than cable.
Upon testing first 3 shifts up from the bottom were perfect then after that it’s double shifting in the middle of the cassette. Then as I get near the top I’m in the 51t with two shifts left. Cable tension is just enough to shift the first shift. Any looser and it won’t move the mech. Getting down from 51t I can barely push the shifter like the cable tension is way too much.
Other than the shifter breaking as I took the old cable out any idea what this could be? Going to buy a hanger alignment tool to check that just to be sure, is the park one worth the extra £20 over the xtools one? 
I wanted it sorted last night but then found a wasps nest in the garage so had to retreat! That’s for the other forum though!
Have you got the inner cable routed correctly where it clamps to the mech?
^that was my first thought reading the OP
I’m pretty sure I have! It was routed the same as when I had it before! Second guessing myself now!
Not at home to check right now but will get a look later. It just comes out the guide bit on the me h and round the bolt doesn’t it?! Anyone got a photo of how it should be so can compare later?! 
Not seen the 12 speed stuff up close, but every other Shimano mech has a shallow groove for the cable.
Yes, I think you've attached the cable to the wrong side of the pinch bolt.
I recently had the bolt connecting my 12 speed XT mech to the hanger back out a bit. Not so much that it caused loads of play and was blatantly obvious, but just enough so that the shifting went off in a sort of similar way to how you describe. Worth checking that too if you didn't already.
I'm sure I torqued it correctly on installation, and did so again. No problems since after about 5 rides, so have put it down to just one of those things.
if it's over-shifting, just going up the cassette, then it's a cable routing issue.
We hastily routed a cable the wrong way to the pinch bolt on a 12 speed xt mech the other day. It did exactly this. Looking at the mech you could be forgiven for thinking the groove is for routing this way.
Wish I had a photo so I knew which way I routed it! Should the cable enter the clamp cassette side if the bolt or outside of the bolt? I hope it’s something that simple!
outside the bolt/wheel side
you are overshifting because the pivot length of the mech arm is too short, so each cable shift is rotating the mech arm too much.
Think of it like a spanner. The longer it gets, the less rotation you get at the nut, for any given movement at the hand end. You have a short 'spanner'. You need a longer one.
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Anticlockwise round the bolt! It's counter intuitive....
I will be back around 5 ish to let you know which way it’s routed then!
Something to look forward to on Friday isn’t it?! 
So hope none of you were holding your breath waiting for me to check.
Congratulations to those called it out, captain rushing the job over here routed cable the wrong side!
It’s clearly working way better now however it still wants to jump up a gear in the middle of the block when peddling, also always drops 2 when down shifting from 51t but I might be able to live with that!
What’s next? Alignment? 
Have you started from scratch with your indexing etc? Has the different mech position thrown out your b-screw alignment?
Will start from scratch again tomorrow. Wasp bloke has just been here and taken care of the little devil stingy things so I’m
Not going out there right now! Gears have always puzzled me. I normally get it close enough but not perfect and just deal with it 
Better find a good video to get watching!