N.B. I may have put this in the wrong section... Feel free to move it if you wish

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Hi guys,
I've been up and down with my MEPIS system, lots of problems everywhere, but I've usually been able to fix them either by myself or with the help of some friendly experts.
This one however, I can't seem to fix.
Let me show you some of my disks:
Filesystem Size Used Avail Use% Mounted on
/dev/hdc1 5.0G 3.1G 1.7G 66% /
/dev/hdc5 16G 8.7G 6.0G 60% /extra
As you can see, my root partition is quite small, and I've been having problems with a few things as a result.
So I decided to make a copy of my root partition and paste it into /extra (/dev/hdc5), then edit the /boot files (both on / and /extra) and the fstab files to make it boot to hdc5.
I had a limited success with this, resulting in me being able to fix another problem with /dev/hdc5 mounted as my root. Now I don't need it as my root anymore (although it would be desirable), and I'm having some more issues...
I've moved my root files back and forth between partitions, and I have a feeling I've lost permissions somewhere in between there. I usually use cp -RfPpv, but I may have forgotten at some point =/. I think it's a permission error anyway...
If I try to use su or sudo, I get a setuid or setguid error. I have problems accessing applications sometimes, and I had to reconfigure my network manually.
Lots of things are simply not working, and it's only happened since I moved my filesystem back and forth. I did a chmod -Rf 1777 / out of deseperation (don't worry, I still have my backup on hdc5 :P), and rebooted, it doesn't seem to have done any good =/.
Please help, this problem is pretty urgent. I'm unable to use my system properly until it's fixed, and I'm well behind on some work for a client (I'm a professional web coder).
Thanks guys!
EDIT:
Doh! Should have given some sysinfo, eh?
Running SimplyMEPIS 6.0. I have the livecd here (which boots fine), but I am unable to burn any other cds at this time (my burner had a heart attack a little while ago :<)
Intel P4 3GHZ, 512MB ram, 2MB cache.
"Spare" HD (sda) is ntfs partitioned, with WinXP on it (which I can't boot), 120GB - 105GB used. I can't resize/repartition/mount it with ntfs-3g or writable in any way because of a "bad ntfs log file" which I'm unable to remove.
"Main" HD (hdc) has many partitions...
hdc1 - ext3 - 5GB (root)
hdc3 - ext3 - 9GB (home)
hdc4 - swap - 500MB (swap)
hdc2 - extended - 22GB (apparently - it's from my old WinXP install on this HD, and QTparted won't let me delete it as it's apparently mounted...)
hdc5 - ext2 (extended) - 15GB (extra)
hdc6 - ext2 (extended) - 1GB (was using it as /tmp for a while to fix another problem)
free space - 6GB (extended)
Help please!
-nfsnobody