Firstly, I'm pretty sure the diff could be mad to fit by using some shims on the control arm bushes to make up fir the difference in width. If not, just get a diff professional to change over the internals, as mentioned above. Oh, and the connection to the tailshafts are different, but easily cahnged.
As for the manual itself. I have a EB box in my EA, so vice versa should be a straight bolt in.
The wiring is pretty simple.
The clutch sensor connection is already located just above the pedal box, so when you install the new pedal box, all you will need to do is plug in the clutch sensor. Its a grey plug.
You will then need to bypass the neutral starter which is a matter of shorting out two wires, this will allow the car to start. I'm not sure of the exact wire colours for this, but I'll find out if ya like.
The reverse lights are a piece of cake. Its just a matter of removing the existion auto loom, and plugging in the manual one, wich should all match up to the gearbox.
The original 4 speed tailshaft and crossmenber can be used.
The ECU should be fine. The auto can work with the manual box, but not the other way around.
I just finished doing a manual conversion to a VL yesterday and I gotta say, there a hell of alot easier to work on then the EA's etc.
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