So let me try to re-itterate what you have said above to clarify it:
You want to place this disk in the system, have it boot up and do all the transferring during runtime while files are still being logged?
I am thinking it will be a lot easier to add this hard drive by first going down to runlevel 1 (as should be in that how-to up there):
Log back in as root, then mount up the new hd after partitioning and formatting at any given location, I prefer /mnt/newdrive simply for ease of understanding (you will have to make that directory first:
Now to mount it:
mount -t ext3 /dev/hdx /mnt/newdrive
Then you copy the data from /var/mydir to /mnt/newdrive and since we are in init 1 now, we will use mv instead of cp:
mv /var/mydir/* /mnt/newdrive
This will in essence put all the data from /var/mydir onto the new hardrive at it's root, but it's root is at /mnt/newdrive (which can be confusing, but will make sense in a minute hopefully).
So now we have a bunch of files in /mnt/newdrive and they were in /var/mydir before. Now we need to umount the newdrive:
And mount it up at the mount point /var/mydir which will place the data right back where it was as if it never left, but with MUCH more room and dedicated specifically to that drive:
mount -t ext3 /dev/hdx /var/mydir
Now if you ls the files at /var/mydir it should appear that they never moved
You can move back to your previous runlevel:
where X is your previous runlevel, probably 3 or 5.
And to have these changes be set in stone on reboots you will add this to your fstab:
/dev/hdx /var/mydir ext3 defaults 2 1
After all that, if you just wanna symlink it all, you could very well:
cp -a /var/mydir/* /mnt/newdrive (I'd pick a more permanent mount point than this though since it will be living at it from now on)
And then remove the directory /var/mydir:
rm -r /var/mydir
And make a symlink:
ln -sf /mnt/newdrive /var/mydir
And this will make it look like /mnt/newdrive is actually /var/mydir for your applications.
Your choice really, the second allows more "use" of the drive should you want to do other things with it (such as add other directories around it and such).