I got all my brake components on and I went to bleed them and all of this black gunk came out of the master cylinder, do I clean it out or buy a new one?

 

At a minimum, flush the system out, but frankly a new M/C is cheap and you have to bleed the brakes anyway, so you MIGHTASWELL...

 

I just went through the same thing... I thought about doing a MC rebuild because the original reman for my 62 was sort of expensive. I ended up deciding that I was better off replacing all of the hydraulic components and switching to a dual-pot master. Then, after I replaced all the hydraulic components, I decided that those old lines were just going to release grunge into my new hydraulic parts, so I ripped out all of the lines and replaced them too.

If the only difference between a near-total rebuild like you're describing and a total rebuild is doing the lines, then I'd think about doing the lines too. FWIW I just finished using the "NiCopp" brand of nickel-copper-steel alloy lines to do total rebuilds on two cars and it was a very pleasant experience -- that's a sharp contrast to all the unpleasant experiences I've had with steel lines.