Hey there, I just put a down payment on the 4 string version of that bass, but I haved played the 5 string version. Here is my assesment, if it helps;
The bridge seems to be a version of a Gotoh. Looks solidly built, has side slots to keep saddles from sliding around, and you can top load, or string thru body. IMHO I would leave that be.
The electronics seem very solid! The pickups are hum cancelling(according to Peavey's website)and to me have a nice fat sound to them. The input jack felt VERY solid-not cheap, like almost every Fender I've plugged into. As far as electronics go, that is always very subjective. I don't plan to change mine. I felt the need to change them in my Fenders though. Again-subjective.
The nut? Only if yours isn't either cut well, or you may be changing string gages from time to time. Again, if there's nothing wrong with it, I'd leave that be also.
The tuners appear to be Gotoh minis-same type used on basses that use this kind of tuner. I had Fender 5 strings years ago with those tuners, and never had a problem. If weight is an issue, you may want to consider hipshot ultralites. The Milleniun is a very light bass however-one reason I chose it-so I don't know if neck dive will be an issue. Of all the mods you've mentioned, this might be the only one I'd really consider, for reasons mentioned above. I have no plans to change mine. In fact, I have no plans to change anything!
The less expensive Fenders are nice basses, but IME, they really can benefit from some changes. The bridges are crap, the pickups aren't the best, and I've found the tuners quite sloppy. Once you change those, then you have an instrument that can compare favorably against a more expensive MIA Fender. Some may have different experiences, I'm just relating mine.
I've found the Millenium to be a lot of bass for the money. I'd say a stock Millenium is hands down a better bass than a stock MIM, and this is coming from someone who has used Fenders for years, and owns 3 MIM's-all modded!
My advice-leave the Peavey stock. If later you decide you really want to change it, than more power to ya'. Ultimeatly, your happiness with it is all that counts. Hope that helps.