Hold on here, your going to many directions here!
Lets start again your system is intact with it's current HD in place and all is well - Correct? OK, if that is so how are you going to replace the HD and copy over the files? you have a few options here.
One way is to make a FULL COMPLETE Time Machine backup. Then restore from it. But, you will need to install a fresh copy of OS on your new HD when you swap the HD's over. Do you have the original OS-X DVD? If not this won't get you very far.
A better way is to get an external Firewire case to hold your new HD in, then use Migration assistant to copy the full image of your current HD over. A variation of this is if you have a new system setting the old system in disk mode acting like an external case held HD then using a firewire cable between the systems image the old system over to the new system.
Yes, you can use a USB connected case Vs a firewire case just takes more time.
Last way is via a network connection (Ethernet) to a file server so hold the imaged HD files then restoring it to the new system. Again, you will need to have your OS-X DVD to do this.
Instead of having your OS-X DVD you could have another external HD or SSD/USB thumb drive device as a bootable OS-X with the needed application files.