For me the stock Baja pickups are bang on the money, I couldn't imagine any better.
My Baja is very heavy, so the overall tone is dark and beefy - those pickups make it a great rock guitar. Three months ago I played a full gig with it, going from Radiohead over Pearl Jam, RHCP, Rammstein to Rage against the Machine - she did all of them rather well.
Maybe, if you're not 100% satisfied, check pickup heights, as SC guitars can be picky about this, sounding flat/thin when too low, icepicky and out of tune when too high.