A couple of things you'll really want to focus on, from my (albeit limited) experience: The first, is rebuild everything on that upper playfield as perfectly as possible while it's out of the game. They give you a cutout on the main playfield to reach the underside of the upper playfield while it's installed in the game, but it's SUPER tight, and nearly impossible to do any real work, other than changing out a lightbulb. Grab a cliffy protector for the VUK ball drop location too while you're at it. Not sure if you've got a smooth surface there, but there's often a divot, and the cliffy protects and eliminates hangups there.
Also, double and triple check the operation of the ball lock/trough mechanism for "no way out;" optos included. It has a habit of cracking, and again, full access to it requires taking apart the whole upper playfield. Also, pay extra attention to the VUK back there too. It's probably the most heavily used mech in the game.
Putting those mantis ramp protectors behind the ball lock standups is a good idea, and while you're at it, buy a couple of target spares. They get hammered. I've already blown through 3 of them. The boulders also take a beating. Get boulder cliffy protectors in while you can as well.
I know this is more of an aesthetic preference, but try to avoid the temptation to place LEDs in the GI for this game. No other game (except maybe BSD during attract mode) uses the dimming feature as much as White Water does. The playfield GI is divided into thirds (lower, middle, upper), and animates in sync to the playfield lamps a TON during gameplay. If you gotta have LEDs, you gotta get GIOCD.
Hope this helps!