When you said that running will decrease your vertical leap, what did you really mean? Training like the athletes train for the olympics? Yeah, that probably would decrease your vertical leap because you're "attacking" different groups of muscles.
But hey, running by itself is a must for you espeacially when you say that you want to improve your quickness. How are you gonna do that, by lifting weights? I don't think so.
It's a good thing that you seem pretty aware of things you need to work on and you have the motivation and determination which are key in this game. In every game basically but you've certainly have seen what does will mean in the game of basketball.
For jumping higher, there are so many things to mention here. You can search the internet for some vertical leap exercises, get your hands on programs like vertical jump bible, air alert or some other ones.
You can visit my website at http://www.best-basketball-tips.com
It's all free and it covers pretty much the things that you brought up. Just make sure to not lose your sight. Keep improving and you'll make it big.
Hope that helps,