First the history: I've got a Motorola SB5100 connected to my wifes PC thru the USB port. My PC's internet connection passes thru hers using a hub connected to her NIC and then ICS.
Knowing that thats not the best way to do it, and after having some issues with ICS, I've decided to upgrade our network by using a router ( Linksys BEFSX41 ) to connect to my PC and my wifes PC, then to the modem.
Wise decision, a router is a better solution than ICS.
Question #1 : The modem ( and I'm assuming my ISP - Charter ) already has my wifes USB MAC address registered, so is it possible to clone the USB MAC address to the router and/or will the modem get confused because its now connected using the RJ45 port instead of the USB port?
Yes the router should be able to clone the MAC address thus avoiding any provisioning issues on your ISP's side.
Switching from RJ45 to USB shouldn't make any difference.
Question #2a : If #1 isn't possible, can I power off the modem for 10 minutes or so, then connect it to the new NIC on one of my PC's, have it pick up the new NIC MAC, then clone that new MAC to the router?
You can clone the USB or NIC MAC but if want to avoid potential provisioning issues you want to stick with the original MAC.
Question #2b : Do I have to call my ISP - Charter, to have them replace the MAC addr. at their end, ( I never had to call them with any MAC address when I first installed the modem - I assume their Setup program took care of it. ) or can I just run the Setup program again?
Worst case scenario yes (if everything else fails). Some ISPs provision to the MAC some don't. If you successfully clone the original MAC to the router you shouldn't have any problems. Or you could be lucky and your ISP doesn't look at the MAC and this whole conversation is moot