Deb, are you referring to the Counting of the Omer script? Please submit a support ticket and I can look into this for you. Thanks.
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Yes, it's for counting Omer.
Yes, you should be able to embed java into a Custom HTML module. Open the module, click on the show/hide button above the text box, that will open up the HTML editor. Paste the code there. I checked the settings on your site so there shouldn't be any problems with this. If it doesn't work for you, please submit a support ticket.