not as simple as it might seem - have a look

soooo, it's disk #1 i want to loose, (second from the top) it's 200 gB and it's old, EIDE/PATA, (same as disk #0) and starting to have bad sectors.
new disk is SATA, 2 tB, in the mail...
my thinking is to, when it arrives, drop it into an external hdd 4x dock i have w/2 open slots - from there i can clone each partition to the new drive, then shut down and ...
but here's the tricky part i want to eventually keep the replaced drive in the tower, wiped and ready for static data storage, (i have a free eide headder) but it is currently slaved to drive #0, while the new drive will be plugged into the separate sata headder ...
do i have a chance here?

will the comp recognize the partitions even though the physical address is different? or rather than doing each partition at a time, can i clone the entire disk to the new one at once?
also of note here, the drive in question holds:
2 linux root drives
one partition holding most of the software installations from 2 windows OSes on disk 0,
linux and windows swap drives
thanks