Those screws were probably what holds the core of the silencer in place. By removing them, the core no longer is aligned properly in the silencer body, and is why you are expereincing issues reinstalling them, and in the performance of the bike. You need to get the silencer open, reposition the core, reinstall the screws, and repack it while you are in there. If a silencer is rebuildable, the end cap will come off of one or both ends, not screws in the middle. I have no idea if that silencer is intended to be rebuildable or not, but anything is possible with a welder and some common sense. Your options are to fix what you've got, or find something else. Your call on whether it is worth it to fix it, or simply swap it out.
By looking at the parts microfiche, it appears that it is rebuildable, but you are doing it incorrectly, the end cap comes out, as I had already mentioned. Since it appears you don't have a service manual (if you did, you could find the proper procedure in there instead of guessing, and wouldn't be here asking), you can view the silencer diagram at
www.kawasaki.com, then go under owners info, parts diagrams, and select your bike from there, then look at the muffler diagram.