Bike won't run right

My brother has a 2003 Kawasaki Ninja and he lost his keys so he took his ignition to a locksmith to get a new key made. In the process of taking the ignition off we had to take both handlebar pieces and unscrew them. In the process of taking the gas tank off we accidentally broke the fuel filter. So after you took his motorcycle ignition and got it fixed we put everything back together and got a new fuel filter now the bike starts and idles fine but for some odd reason wouldn't rev up into the high RPMs. After changing different gas lines because some were kinking up we got the bike to where would finally go up into first and second gear but would start to bog at the same point we honestly have no idea what this could be because I wouldn't think that six inches of gas line would make a huge difference we tried it with a new fuel filter and just directly to the fuel pump but it still wants to bog down. all we did was pull the tank off and loosen up the handlebars we have been working on this for the last 2 weeks and I don't know what to do now if anybody has any suggestions please let me know thanks. And yes the bike was running perfectly fine before any of this.