Hi DaveLooking at your post I read it as:-
you have a new hard drive and a new mainboard.
you xcopy'd the existing system from old hard drive to new drive.
Regarding sound: AC'97 is not an audio chipset; it is a specification for an audio chipset. Therefore while both mainboards involved may have AC'97 sound and both may be supported by uniaud they are probably 2 totally unrelated chipsets.
So, you have uniaud installed for mainboard 1 but you are now using mainboard 2.
The only answer I have ever found for this is to reinstall the uniaud driver - I suggest the 114RC2 version may be worth a download from ftp://ftp.netlabs.org/pub/uniaud/uniaud114rc2.zip
You may also need to use a mixer to check that output and input switches are on and volume is set once booted. I use the PMUnimix mixer from http://hobbes.nmsu.edu/pub/os2/apps/mmedia/util/mixers/umixpm2p1.zip
You may find that this mixer peaks your cpu so you need to Right Mouse Button click on the mixer when you 1st start it and select Less aggressive from the menu.
For help with USB I am going to refer you to a little USB Configuration Tool that comes with a help file and a USB Removables FAQ. I suggest a read of those docs before attempting any changes. USBcfg is available here
http://hobbes.nmsu.edu/pub/os2/system/usbcfgb7a.zip
Hardware Manager shows that your controllers are Enabled. What else do you expect?
If you are looking to discover what you have plugged into those controllers then you need to use either USB Resource Manager or USB Dock. They obviously do not show anything if there are no devices plugged in - note that devices plug into ports which are connected to controllers 
As you have eCS1.2 you probably already have USB Resource Manager installed - check the Programs -> Utilities folder.
USB Dock is only available to eCS Software Subscription customers through the ecomstation betazone and is basically a replacement for USB Resource Manager.
Hope the above is of help
Pete