There is quite a lot of patches in AmiKit, that could cause your problems.
1) Remember, that when copying stuff directly from AmiKit, that there are some versions of software compiled for 68060, while versions in AmiKit are usually for 68020 etc. You can ofcourse get much more performance out of your machine when using correct libraries and utilities
2) Check that if there is some program doing something that requires switching between 68k/PPC - if it is every second, maybe you have some sort of screensaver polling, clock or taskmanager etc. Especially that MemTrailer -patch that is used in AmiKit might make your Amiga slower.
I recommend you to take AmiKit as a guide, do not copy directly from it. Look it one (utility/library) by one, check if it useful for you in emulator and then download best version of it for your real amiga.
