fitting brake lines to MC
Something to get straight: the master cyllinder is cast iron, and the brake lines and fittings are steel. They are easy to cross thread because the angle the brake line is bent, is the angle that the fitting will want to screw on. Been there and done that.
If you have cross threaded and munged up the master cylinder threads, I wish you luck. You might be able to remove the master cylinder and clean up the threads with a steel pick or some such tool, but I don't know what the thread pitch and diameter are. It seems by my recollection that the threads are an uncommon size (maybe unique) and don't think there is a thread restoring tool or tap you could use. Could be wrong thoough.
As for cleaning up the fitting on the end of the steel brake tube, you can buy short lengths of brake line that have fittings on both ends that you can essentially splice in. Some experience with a flaring tool would be useful. If you haven't done this and are not confident of your capabilities, it is a job you may consider leaving to a pro.
Between the MC and brake line threads, the latter will be more easily taken care of. Next time you reinstall brake lines, make real sure that the fitting is well and truly lined up to the master cylinder. I know it's difficult if your brake line has been beat up a little and is no longer straight or round, but it's important and you can come into quite some amount of grief if you cross-thread these things.