OK, I tested the car today and here's the deal for those of you playing at home.
I was thinking that it was a fault that had occured causing this to happen to the box.
I was wrong. This has been happening since the box was rebuilt/repaired/dodged up by some noob who fitted the wrong first and second gear for the rest of the box. It would have been plainly obvious that 2 and 3 were the same size.
5 speeds have two pairs (1&2 then 3&4) 5th is all alone.
So it is possible if you're stupid enough to mix gears from these two boxes.
v2 Ra Close box = 3.454-2.333-1.750-1.354-0.972
v3 wide box = 3.166-1.882-1.296-0.972-0.738
to get this = 3.166-1.882-1.750-1.354-0.972

After a short drive, I'm confident that's what has happened. There is no noticable difference in ratio between 2 and 3. All the top 3 are close ratios too, and the gearing is short in 5th.

The easiest solution is to get hold of another box and fit it, confirm what the rear diff is because you can't trust that it matches anything either.

Those Ra 1-2 gears are just about impossible to get these days, and they were never suitable for everyday use anyway.

Dodgey Spec YO! Super Awesome double 2nd gear.

__________________
RS Liberty - Because WRX's are only good for parts...

Doug my friend, props to you for finding this problem. your a legend.

Now I've seen everything!

Wow!

Any chance of posting a video of the car going through the gears, so we can hear the ratio issue?

Yep! Super awesome because when you're fully sik street racing a Skyline and you hit the NOS and blow second gear, you just use the spare second gear! Why didn't we think of it earlier?