I am using Joomla 2.5's built in contact info display function, and when viewing via MobileJoomla Elegance template, the email addresses display incorrectly ( using "(at)" instead of "@") and additionally, the telephone numbers are plain text and not a 'tap to dial' format...

Considering that you charged me $70 to download and TRY this template, I would have thought you would make that function a built-in feature at least as a select-able option.  Am I just not seeing it somewhere?

Additionally, I have a module in my site that isnt compatible with MobileJoomla.  Why can I find an option to exclude the page of my site using that module from the mobile web format?

I would think these things would be basic for a product you are charging twice what your competitors charge.

Please advise.

"(at)" instead of "@" is result of email cloaking (note that link itself works well, and after click mail application is run with correct prefilled email). Unfortunately, default Joomla's cloaking method is not compatible with AJAX navigation (because of call to "document.write" method) and we had to override it with AJAX-aware implementation.

As to phone numbers, you can wrap them into corresponding <a> tag, e.g.:
<a href="tel:+123456789">Call us</a>
This way works on all devices. Autodetecting of phone numbers in browser is disabled, because of it often transforms any set digits to a phone number.

In Mobile Menu module you can list IDs of menu items that should be hidden from menu (but they can be accessible using direct links). Alternatively, you can disable some modules and/or plugins in MJ settings page. Another way that may be helpful is to use Mobile Content plugin (www.mobilejoomla.com/extension/advanced/mobile-content.html) to set different content for desktop and mobile devices.