I've just removed the brake and clutch master cylinders from the donor, and unscrewed the hard pipes from both. The fixings are currently still on the pipe as the end of the pipe is flared. Should I recover the fixings, or should I buy new when I get new pipe?

For the small cost, I'd get new ones chap, it is your brakes after all (and clutch )

As above.

Generally when stripping a donor brakes it is better to cut the hard brake pipes very close to the pipe unions with a pair of side cutters and remove the pipe fitting on the bench. Doing this makes it more likely the pipe fitting will unscrew without thr hex rounding and also keeps dirt out the component.

May I suggest using a Sierra master cylinder without a servo is not a good idea as it will result in the the pedal pressure required to stop the car being much higher than anything you have experienced in a production car, using a more suitable smaller bore master cylinder from a MK1 or MK2 Fiesta or a Fiat is a better way to go.
If you do a forum search you will find many threads on the subject.

The donor is an MX5, so I want to try and use both master cylinders as they came off the car. Good point about the dirt though, they're currently just sat on my garage floor having removed them late last night. The unions came out quite clean, only one corner rounded but it came off when I moved round sixty degrees. I won't reuse them, but I will go recover them and temporarily refit them so things stay clean.