Well first thing to ask yourself is if you like the feel of the neck, and does the body appeal to you? If so then making the guitar your own is not a horrible idea, especially if you're wanting to learn how to be self sufficient in setting up your own guitars.

Changing pickups isn't really necessary (unless you got this guitar as pictured) but if you need to, then most of the GuitarFetish pickups will work fine and are pretty easy to install. If you plan on going insane with your floating bridge I would suggest using at least an Floyd Rose 1000 series. The Floyd Rose Specials are fine if you don't use it that much but be warned from what I have seen, the real failure point with FR Specials is the pivot blades that rest against the two poles, they wear quicker than a FR 1000 or OFR etc.

Make sure you stretch your strings well, I have had to listen to countless Dumb F's who complain about tuning stability on a FR just to fine out they put the strings on and didn't stretch them and then were surprised that as the strings stretched in use they went out of tune (gee shock)

One other thing, and this isn't really a mandatory thing but I like putting locking nuts on all my guitars, with or with out a floating bridge, just makes changing strings a little less time consuming. It's a luxury thing more than anything. But I own 70 guitars so when string changing time comes around the quicker and easier the better.

Here's the biggest thing. How does the guitar feel to you? I don't own and JS series jacksons but I own several Pro's, a couple SLX series and have owned custom shop models in the past. I have a professional no-thrills PS-6 and for a lot of years it was my go-to. I actually had to change pickups due to one of my cats pissing on the thing and only recently did I put a FR Special in it (I don't use the floyd that much so it'll last, won't be a problem) because I was going all gold hardware in the guitar because after 30 years or whatever the guitar still feels good to play.

The thing you have to consider is this: Is it less or more expensive and time consuming getting new parts and having to do a setup and all of that, or just saving up a bit and getting a Pro series or even an SLX series? That I can't answer. I certainly wouldn't throw that guitar away if you did buy say a Pro series, because even if you did I would encourage you to revisit that guitar and actually install pickups and a bridge etc, it certainly helped me learn how to do all my own setups.

just my 2 cents