It sounds as if you're having overall SPEED issues that are probably unrelated to Flash or Java at all.
The first thing that I would address is the slow boot/shutdown time. Take a look at ds store's excellent user tip - Why is my computer slow? It may provide some tips to getting your Mac back on track - if not, also see Mr. store's Step by step to fix your Mac.
You might also just want to check your download/upload speed to see if that's what's causing your Internet connection to flake out - try http://www.speedtest.net/.