So my friend gave me a One Pick-up Epiphone Junior with a broken neck.

Aka, a good first project guitar to customize and start on.

I want to get a new neck, put on a pick guard, put in a second pick up, Cool knobs.

Make it metallic or metal looking, or put a graphic on it. Cool paint job.

How much might all this cost? what do i have to know? I want to turn this dead little guitar into something unique i created. any helps appreciated.
depends on how much you want to pay on this stuff. If you go to mighty mite, you'll pay alot less than at warmoth for a neck, and other such things. pickguards also generally depend on what you're looking for, there's $20 plastic ones, and $100 stainless steel ones. knobs are generally cheap enough.

if you want a cool "metal" looking finish, you could stick a piece of diamond plate on the top, then get a black plastic pick guard over that. that'd probably look cool.
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you could also get a blowtorch onto the body
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I play in drop F. When I chug on the 6th string the floor splits open and satan crawls out.
depending on how broken the neck is you could actually repair it yourself/start a relic project if you're into that sort of thing

if you repair it correctly it'll be tough as nails
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Yeah man, a picture of the neck break especially - I've fixed loads and if its done right shouldn't cause you any future grief

As for cost, it really depends on the quality of the end result. Not that the more you spend the better the gear but do some research before you buy the stuff cause quality varies massively on stuff especially the electrics you can pay peanuts or you can pay through the nose to vintage spec wiring looms that'll "make it sound like" whoever but really your the best judge on what to use.

My advice, get a complete idea in your head of what you want then make a build list, price it up and where it's all coming from then post it on here and we can give you some advice before you spend anything or offer cheaper/better alternatives to get the same result