So its fixed but I thought I'd post here just in case anyone else with no car knowledge has the same problem and makes the same very simple mistake.
When adjusting the linkage you have to remove the slack from the cable so I was pushing the cable into the end catch as that seemed like the correct way. What I should have been doing was to pull the cables away from the shift end cable catch's.
That difference of 3-4mm on each cable made the difference of the mess I described above to it now working in all gears. I'm pretty happy as I was going to call a mobile mechanic later today.
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