Sorry to resurrect the dead here, but I wanted to add my 2 cents for those still looking into this topic.
I just upgraded the fork on my 2008 Specialized Stumpjumper FSR Comp from a 120mm FOX RL to a RockShox Sektor Gold RL Dual Position Coil fork. It is a 150mm fork that is adjustable to 120mm with a switch. It's super sweet. The total fork length from axle to crown on the RockShox is just under 3 inches taller than the FOX. That sounds like a lot, but I don't really notice it when riding. The 120mm mode makes it almost identical in length to the stock FOX fork, so no change in geometry for climbs. Going downhill is much better. I feel a lot more confident in steep, rocky descents and the handling feels almost the same. I wouldn't say it's gotten worse; quite the opposite in my opinion. I have yet to really test it out over time and multiple trails though.
My only concern is the integrity of the steering tube on the frame. The rake is bigger, so there's more force on the steering tube. The bike, though, is designed for a person that weighs as much as 300 lbs. I only weight 200 lbs, which is still heavy for a bike, but much lower than the max weight for the stock bike. So, aside from the age of the frame, possible stress and so forth, I don't have any real concern for the frame.
I know Specialized doesn't condone increasing travel more than 10% or whatever their stupid number is, but that makes no sense. They should specify an axle to crown length, and that value should increase/decrease as rider weight decreases/increases. The main point is force on the frame. So rider weight is the biggest factor, IMO.
So, if anyone is thinking about upgrading their front end to increase the travel of their older stumpy, I say go for it! I'm stoked I did. Plus, I had forgotten how nice and plush coils are. And the Sektor Gold RL isn't much heavier than my old FOX RL.