Jonathan, I've done the Lax-Narita-Singapore-Bali 4 times. Never had a problem with my luggage. They check it thru at LAX.
Regarding the Wakatobi rep meeting you that is after Customs and the $25 you pay. Check with your TA but they should have a person meeting you when you get out of the customs area. It would not be a Wakatobi person unless you booked the Hotel thru Wakatobi. The next day depending on what time your Wakatobi flight leaves (you'll probably have Crispin's number to call) you will arrive at the Domestic terminal once inside there should be plenty of Wakatobi people around to get you checked in and up to the Lounge.
If you just e-mail Crispin crispin@wakatobi.com ahead of your departure, he'll have someone waiting for you before you get to customs, regardless of whether you booked your hotel through Wakatobi or not. We actually landed, had someone from the resort meet us and get us through customs, then took off for 5 days in Bali before shuttling to the resort. As long as you're eventually going to Wakatobi, they're happy to meet you.