I did the same thing. I bought one as a beater bass to keep the garage. I normally play USA Fenders, etc.
I bought the SX SPJ-62 Vintage White. The finish and fit is perfect! I hate that, cause it makes me question my Fenders...
Joking.. I agree with the nut being too high, and the truss rod was loose, probably on purpose for shipping.
I filed the nut slots down, tightened the truss rod about a turn and a half, lowered the pups (cause of the click you mentioned... strings hitting the poles), then installed some Labella Flats... The bass actually has a perfect setup and feels great!
I won't be modifying this bass at all. Serves the purpose of what I bought it for and more, but I can see why people decide to throw in a little cash towards upgrades on these.
As I said, it's a beater bass for me, so I'm trying to not care too much about it (but it looks sooo good...

) ... I mainly play it in the garage when hanging out there, plugged into a small Peavey Amp. Worth the $99 for sure, especially when I consider that the Labellas I have installed cost $49 new at a local shop, which really makes the price of the bass stand out as the deal of the century!