I'm starting to lose the plot with this gearbox

After having it repaired (selector shaft jammed up with swarf from a damaged fork) and finally getting my car back on the road with its new zetec engine it is still giving me issues.
I'm running a hydraulic clutch conversion with a brand new AP clutch. The biting point of the clutch is in the first 1/4 of the pedals travel. The gearbox has exactly the recomended amount of Ford specific gear oil in it.

Changing into 2nd, 3rd and 4th feel really notchy, almost like pushing it through a edged gate. Could this be down to the linkage not being aligned correctly?

Everytime I adjust it the gear change feels absolutely fine on the driveway, until the car starts moving then it seems to get worse and worse.