Stu,
Were the gearbox and levers in the car and working previously? Looking at my FB it damn near fouls the tip of the slave, but not anywhere near as much as yours looks to be.
Not sure what you mean by "when I try and put the column gearshift in it is nearly hitting the dashboard" - do you mean that the whole gear lever is very close to the dash when you try for 2nd/3rd??
The grey motor crashbox is fitted with two external levers - a shifter lever (the one nearer the front of the car), and a selector shaft control lever (the one near the back of the car). One thing that may make the slave cylinder foul is the selector lever. The selector shaft control lever changed in length (became longer) at the FE Holden model (FX-FJ Holdens use part number 7400177, whilst FE-EK Holdens use 7409290 for right hand drive). Your FJ gearbox may still have the (shorter) FJ selector shaft control lever hanging off it, which will pull the rods closer to the slave. The image below shows (from left to right) a FX-FJ Holden selector shaft control lever (this might be your problem), a FE-EK Holden selector shaft control lever (longer, moves the rods out further to clear the slave), a FX-FJ Holden shifter lever, a FE-FC Holden shifter lever and a FB-EK Holden shifter lever.
If you do have the shorter FX-FJ lever, and want to try the longer one give me a yell and I'll dig one out of the Spare Parts Department.
It would be pretty hard to mix the two rods up, as the ends are twisted different ways. There is a rough chance you have the wrong rods though (no guarentees on the one I dug out for you

). Worthwhile checking dimensions as per below (note that FE-EK are identical, I have no dimensions for humpies though):
Dimension FE-EK Holden
A 10.01”-10.99”
B 7.27”-7.29”
C 10.57”-10.59”
D 21.55”-21.57”
E 23.41”-23.43”
F 10.25”-10.27”
G 7.63”-7.65”
H 7.77”-7.79”
I 18.69”-18.71”
J 20.67”-20.69”
Cheers,
Harv
327 Chev EK wagon, original EK ute for Number 1 Daughter, an FB sedan meth monster project and a BB/MD grey motored FED.