I bought my first and only needed bass about a year back from a second hand store. It is a Fernandes. It came with a document that stated the bass was originally bought back in 87' for a bit over $2,000 AUD. Now I don't think the pickups have been changed since then because I can't find much about the company (for you who care the company is F.G.I Technology)

I'm very new to anything related to pickups so as much help as you can give will be greatly appreciated.

The tone I want: I dig John Myung's clean deep badass tone, but I also love upped mid powerful heavy stuff like most hardcore bands and metal. For those of you who know Municipal Waste, I want that sort of tone as well. I like to play a bit of funk slap so a tone that can do that would be amazing.

So is there are there a set of pickups out there that can been clean and deep yet low and powerful but also bright and funky?

Not to be a debbie downer here but how much did you pay for this thing? NEW Ferndandes basses don't even come close to 2000 dollars, and that's with inflation. I am hoping you didn't get ripped off big time.

Onto answering your question. I find that Bartolini pickups tend to give a lot of the clean deep and powerful tone that you may be looking for. They can also do bright and funky though not as well as some other companies. Bartolinis are very smooth and deep though, and that seems to be what you're primarily interested in.
I payed $300 for it, but seeing as guitars are much more expensive in Australia than most other places, that's like a $100 dollar bass in America.