If I understood the writing correctly, looks like these are originally either 640GB platters or 667GB platters. It would be nice to buy a three platter 2TB drive.

I don't quite understand the issue here. Wouldn't the 40GB be upgraded to 80GB? The only major issue I see would be the performance, since the number of channels would be the same. But hopefully other factors from the 25nm would come into play to make the new 80GB to perform as well.

What I would do is to disconnect all the older hard disks, then install. The new HDD will then claim C: and D:. Later reconnect all the other hard disks, make sure that the BIOS is set to boot from the new hard disk and boot up. The new OS will then see the older hard disks and assign its own drive letters to them.

lms2005, hard disks can read/write up to 150 MB/s, USB 2.0 can transfer data up to 30 MB/s and 1 Mbps Streamyx can transfer 125 KB/s (theoretical). You really don't need to worry about hard disk performance issues when it comes to Internet activity.