I think you will need to do a good deal of study and work to accomplish this. It's far easier to watch all your recorded shows (or record them for later) and then start with a new drive and dload the system. If your HD is flakey, you could have errors which you would propogate to the new HD.
I have done hot swaps and used winhex, which I bought. Instead of hot swapping the IDE cable with one connected to a pc - and then boot the pc, I've used a usb enclosure. It usually takes a couple of trys before I get it to work, however. But I prefer this to opening up my pc and messing around. Also, no pc bootup is required this way, and winhex easily sees the new usb drive.
(there's some cheap usb connectors w/o an enclosure at frys that don't have an actual enclosure, just some cabling and a 3 headed connector for 3 kinds of drives - plus an external power supply - perfect for this sort of tinkering).
However, I did blow out one of these enclosures once and I often feel some tingly electrons when I try to push in the cables (note that there's two sides to ide connectors if the connector is at the end of the cable, and you can get zapped if you touch the side of the connector where the ribbon cable has its exposed ends).
I do seem to recall that long ago someone had actually cloned everything, including saved shows, and that you're right, you can use a larger disk, but it will not actually use that space - since by cloning you also clone the partition tables. I've never done this myself, I only copy portions (the o.s.) from the utv drive to/from the PC.