Shane,
I really don't know Ecwid, so can't guarantee any answers I give. JFBConnect does have Like and Comment buttons built in. I'm not sure how Ecwid adds them to your pages or even how it works in general. Can you edit the template files for how your pages are shown? If so, you can easily add the JFBCConnect Like & Comment tags.
Ideally, you could actually use the Ecwid tags that are already there.. however, the re-inclusion of the javascript library is the problem. If the only way to disable the Javascript library is to disable the button and comment box, you'd need to manually re-add them using JFBConnect. We can gladly help you to do that though.. but just may need your assistance in understanding Ecwid a bit more.
Thanks,
Alex
Clicking on "Login with Facebook" does nothing
I didnt think of it because its not hosted on my site its pulled from the ecwid site via java script. Disabling the Like buttons and comments worked. However im a bit stuffed now bacuase i either have to go without like button and commenst on my ecwid store products (which effects anywhere else the store runs on like google sites and facebook) or go without facebook login 
