Alright, now that I recreated the problem, I will proceed with the fix:
How-To: Root a Custom ROM: A bin named 'su'
The issue is that the installed su binary is not doing something right and the /system directory is now again read-only.
We know that the installed Superuser.apk 3.0.4 provided by Kraven, combined with the busybox and previous version of the su binary from the ZVD rooting guide work just fine together. However, we cannot overwrite the faulty su binary with things the way they are.
So we refer back to
Drew's guide to ZVD rooting for instructions and for a copy of the version of su that we know works.
We need to use adb to push su and gingerbreak only to the device. I am going to presume that you know how to fire up adb, since you already had a rooted a ZVD-based device.
Note
Even though you may get a # prompt in adb here, you are not running with root permissions and will get an error if you attempt a command that requires them.
Skip Step 3 in the guide, as you may want to keep some things your custom ROM has there. if If you are curious or cautious, you can use the following command to see what's there:
Go right to Step 4 and
push only the provided su and gingerbreak. to your device's /data/local/tmp directory.
Code:
adb push gingerbreak /data/local/tmp/gingerbreak
adb push su /data/local/tmp/su
Follow Steps 5 through 10 exactly.
At Step 11 and Step 12, only cat the su file.
Code:
cat su > /system/bin/su
chmod 4755 /system/bin/su
Exit as described, reboot and enjoy!
Superuser may prompt you for permission if you have apps that start at boot.
Go use your favorite music app to listen to the Johnny Cash song that is now stuck in your head.