Mike - I have the same problem as you re Scenic gear linkage having taken engine/gearbox out when swapping the engine over (cambelt snapped). I also read Haynes manual and didn't glean much from it. Anyway, did you basically do this by trial and error? Currently I can't get reverse - it goes into first when I lift the 'collar' up on the gearstick. If I don't lift the collar, it goes in to 3rd. Any tips gratefully accepted, thanks - ChrisJust in case anyone needs to do this I thought I would just explain how I got on. I read through the Haynes description and was none the wiser, so jacked up the car and got under to have a look. My scenic has a rod connection from the gearstick to the gearbox selector. Just to explain that the gearbox selector has to move in two planes, obviously forward and back to give gears 1,2,3 and 4 but also up and down to be able to get reverse and fifth. Both adjustments are made by slackening the pinch bolt at the engine end of the selector rod. By lenghthening or shortening the rod you adjust the "throw" and by twisting the rod you adjust the "up and down" movement.
The Haynes manual goes into great detail about using a shim of a known thickness and locking the gearbox in gear with or without a special tool, with the pinch bolt slack the clamp will then find its own correct position. This did not work quite well enough for me and I had to "tweak" it a little to get the correct centering of the gearstick in front of 3rd gear.
The important thing to remember is make a mark so you have a point to return to and one which shows you how far you have "adjusted" the clamp. Also, millimetres make a difference between being in and out of gear. Keep going until it feels right, having someone in the car "trying" the gearbox between adjustments also helps. :d