I don't think I've ever heard a USB drive that "clicked", as there aren't any parts inside that move. I could be wrong.
Is it possible that you're hearing something else?
BTW, even though the iMac is booting and running fine from the USB drive, you need another copy of your files.
I'd suggest shopping for an external drive, or perhaps a USB3/SATA docking station.
It should be USB3. Even though your current iMac doesn't support USB3, at some point you'll probably own a Mac that does. And remember that USB3 is "backward compatible" with USB2 as well.
I'd suggest a USB3/SATA docking station, myself. They aren't as elegant as an external drive case, but they're VERY useful devices. To see what I'm talking about, go to amazon and enter "usb3 sata dock" in the search box. Many choices, some as low as $20.
Then... get a bare drive to go into the dock. You might even consider one of the 240gb SSD's, which are very affordable right now. You won't get all the speed possible by running it as an "external booter" with the old iMac, but at some point in the future, the speed will be there for you.
Once you have the dock (or enclosure) and a new drive, use CarbonCopyCloner to clone the contents of your USB flash "boot drive" to the NEW drive.
Now you're backed up...