Hi Jack,
You need to remember that even on carbs the 3.9 will have a lot more oomph than the 3.5 you are taking out (it is a low compression unit). Brakes steering and suspension need to be top notch or you will end up with a 100mph death trap.
Lots and lots of info for your rebuild, what do you want to achieve? In the vehicle you have I would suggest you don't go far from standard spec becuase of the reasons previously stated.
For parts I suggest you go to Real Steel or LR genuine for rings and bearing shells - do not cut corners with pattern stuff it will only end up being a massive waste of money. Buy right and buy once.
You will need a new cam and followers, LR gen for the followers and something like a Piper 255 for the cam (better value than LR and it will be around the same spec as standard). Genuine for timing gears and chain. There is a strong likelihood the rockers and shafts are tired as well, again genuine ones are the only source of reliable quality for standard type engines.
If you want a nicer end product and a little power gain it is worth having the pistons, rods, crank and flywheel all balanced - much smoother and cleaner power delivery. Engine services in Rosewell are very good, they balanced my 3.5 when I had it rebuilt by Rocket Sled tuning.
Heads are probably not worth starting to play with much, 3 angle seats and minor smoothing will give quite big gains in power for relaitvely little work although to be done correctly a good machine shop will be better than amateur mechanic. If you start going to these lengths you will need disc brakes on your car.
A little more info on your aim would be good, to do a proper standard rebuild yourself I would have £1k ready to spend to avoid disapoinment.
HTH
PS Is the injection kit up for grabs with the ECU and air flow meter? I'm upgrading from carbs to efi and need all the 14CUX hotwire bits....