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 and friends, 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.
