I had low-oil alarm issues that turned out to be a really odd problem that I never really totally diagnosed. There are sensors in both tanks that work together to send the signal for more oil. Since the emergency switch works, your oil pump is OK. The service notes has the procedure to test the sensors. On Yamaha's prior to early 2000's, I believe the oil pump control module was a seperate unit. On mine (2004 150), they built it into the CDI. Signals from the sensors go to the control module to turn the pump on and off. But don't overlook the obvious such as oxidized connector contacts anywhere in between.
For my problem, when my alarm sounded I'd manually fill the main tank using the switch and it would run fine all day. Problem was when I tilted the engine back, overnight or until I got back to the boat, the oil in the main tank would siphon back down to the resevoir in the bilge. When the engine is started, the control unit automatically runs the oil pump for 90 seconds or until the main tank is full. Problem is, it's a low volume pump and would need more than 90 seconds to prime the now empty oil lines. Essentially, I'd start off with low oil and it would stay that way until the alarm sounded. My fix was to put a check valve in the oil line, since there was none and the Yamaha manual didn't show one. I had the boat 3 full seasons before this started happening, and I never really figured out why.
Just something to think about. Good luck.
John S.