Wheel Well
I won a spare wheel well of ebay to put on the new body as it has had the well cutout and a flat piece of metal welded in place. Picked it up yesterday, $40 + $30 postage.
New Clutch and Oil Change
The new master and salve cylinder didn't completely fix the problem which pretty much meant the clutch needed to be replaced. There were 2 different clutches listed for the 260z from Repco. I ordered part number R63N as I already had an old box for one at home and figured it was the one I needed. Turns out this one is for the 240z, the 260z required a taller pressure plate (and a more expensive one, $230).
So I took the clutch back and they supplied the other part (number ####) however when I got home and opened it up it look like it had been used. Finally went back the 3rd time where they swapped it for an Exedy clutch for the same price (RRP $270). Got the gearbox back in and whilst it was up on the stands I did an oil change with a new filter.
Car is now back up and running again.