R6's (the current gen) sit higher in my exp. I'm typically a one foot down at a stop light kind of guy myself, so a bike would have to be super tall for me not to want to ride it. That bike with 30k+ miles and it being a 2001, you may get $2500 (imo) if its immaculate and has all that maintenance done. Maybe less if the valves haven't been checked. Unfortunately it's just an older bike. You'd be correct to sell it during spring time though.
My daytona has 31k and I'm about to track it this weekend. So long as a machine has been properly maintained it shouldn't spontaneously combust if that is what is playing into your decision to start looking for something else.
1000's are a completely different beasts, especially the s1000rr's. Not to scare you away from a liter, but just warning you. You can get in deep really quick on a liter bike.
Lowering changes the chassis/ steering geometry. I've never lowered any of my bikes, I've ridden lowered bikes, in my experience the lower the speed, the more you feel the bike has been fucked with. Still not my preference as you have less ground clearance as well.