Thank you, Almost everything I was having issues with is fixed in version 3.2 however...
I've updated to CleanMart 3.2 and I am still having some issues with the Alternate Ship To address management.
Selecting an alternate address Radio Button works "some" of the time, however, if I select an alternate address, then select the default address, then try to select an alternate address again it doesn't update. I've also had situations where right after logging in and adding a product to the cart I am not able to change the address, However if I select an alternate address radio button, then Select "Show Cart" again in the cart module, the address I selected previously now shows as selected...
I've done the same test in pure VirtueMart with CleanMart disabled and it works fine there.
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Update: 3/10/15
After further investigation I've discovered that there are still some remaining issues with Virtuemart handling of alternate ship to addresses. I am in communication with their developers and they have provided a partial fix so far. They are working on the remaining outstanding items now. I believe that the above issue seen in CleanMart will go away once Virtuemart is fixed.
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Also, with Ajax loading enabled, if I attempt to checkout without having selected a Shipment or a Payment method, I get taken to a page to select either shipping or payment methods, or both, depending upon which I leave blank. In all cases when I am taken to these pages the "Save" button has no effect. All you can do is "Cancel". The same issue is also there if you disable Ajax loading of shipment and/or payment in the plugin - you get taken to an appropriate page to select either shipment or payment but the "Save" button does nothing.
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Update: 3/10/15
I've made some minor changes to the select_shipment.php and select_shipment.php scripts that fix this I also had an issue with a missing "</div>" tag in both files that was messing up my template when either of these scripts was displayed on a page. I'll send them along in a PM for your review.
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A minor nit - on the Cart page there is an errant "?>" just above the "Cart" title. (Line 77 in com_virtuemart/cart/default.php)