There are other topics on the forums here concerning missing programs from the menu. I don't know what misssing files you are describing. Do a search on the forums here for some solutions that have been offered. But kde 3.2.2 comes with a menu editor and a menu updating tool. If you use them, you will find programs you can add to the menu.
Since I am now using the beta 3 version of Mepis, I have kde 3.2.2 working right. The beta 3 comes with kde 3.2.2 and I don't see any problems with it. When I used the latest stable version of Mepis, I had to upgrade to kde 3.2.2 manually to get it and there were some bugs that I had to fix. But there are no bugs in my beta 3 version concerning kde. At least none, that I've come across yet.