As described above, you can’t just copy all of the old files back into /etc and expect things to work properly afterward. Some files you can do that with; for example, /etc/XF86Config (as long as you’re using the same version of Xfree86 — and the same video hardware — in the new installation as you did in the old). For the most part, though, it’s best to use diff to compare the old and new files before doing any copying. Watch out especially for significant changes in the files in /etc/rc.d, which may require you to reestablish your old configuration by hand editing, instead of by copying the old rc scripts from your backup. Once it’s all done, reboot.