The negative spring was the go for a while back then , Simons kits and Forks as well as Fox Forks had then . They just act against the main fork spring and make the initial travel a bit softer , more progressive . The front end also sits a bit lower . Nathan is right in that Yamaha used to calculate this in the overall fork travel , the front ride height is lower so you don't use all the travel that they claim when you hit a bump but the fork should extend a bit further on rebound after the bump and the theory was the front wheel would therefore follow the ground a bit better.
I would also check the actual travel first.I would take the longer softer neg spring out and measure the travel with the forks fully extended to the top out spring , the take the neg spring and compress it fully in a vice and measure the compressed length then take this measurement off your fork travel already measured without the neg spring . That's your actuall travel then chuck the neg spring and make a spacer long enough to reduce the travel back to 9".