DMCC, I've done a lot to my bike - excepting carb & porting. I've got gold valves in the front, but have no idea how they compare to stock - the bike came with them (previous owner was a sponsored Kawasaki rider, all other additions he put onto his next bike). I got a softer spring for the rear, but have left the stock fork springs in. After coming up 3 years on the bike, I'm about to get it lowered.
Am I throwing good money away on a 4 year old bike? I don't think so. I intend to keep her another 2-3 years and if lowering it makes riding the bike more enjoyable, it's worth it. Yeah, I could go out & buy a new bike, but I don't want to at the moment. Is there any point in me lowering the bike, after all, it's obvious I can ride it at the height it's at now? For the 1-2 times a ride (if that) that I get myself into trouble because I can't reach the ground properly, I think so. The person who's lowering it has been on my case since I bought the bike and as I can't think of anything else I want done to it, decided while I'm not riding for a while, why not try it.
Basically, what I'm trying to say in amongst the waffle, is, if it's going to help you or make your riding more enjoyable - go for it. You're keeping the bike long term, you're going to lose money if you do go to sell, but what the hey, additional enjoyment has to come into it. Stock suspension sucks. I remember I could hardly wait for my new shock spring to come to see how much difference that would make & was thrilled at the difference (my YZ80 had had the suspension set up for my weight, just not my ability - but even I noticed the difference when I got the 200).
Let us know how it goes.
Michelle