Bearing in mind I have not done this...
1. No, you will have to initiate formatting. Menu >> Settings >> System >> Data Storage >> Format Storage
2. Not the custom firmware itself, it will drop back to the web installation screen stage.
3. I don't think so. As far as I know, the only things (not counting the custom software) stored on the hard drive are the actual media content, TSR buffer, streaming buffer, DLNA index (rebuilds automatically), EPG (rebuilds automatically), and the cookie file (who cares?). Everything "important" is stored in the flash drive.
4. As above.
5. I hope not. The main trouble you might get into is if the Humax refuses to format the drive, and then you might need steering through it.
You don't actually need to save your content off, if you have a USB to SATA adapter (or are prepared to buy one) you can hook the old drive up afterwards and copy across from there. Ditto the custom firmware (using the command line; Telnet will survive the drive change).