Thanks for the suggestions. For item 1, I’d make it an optional checkbox in the admin.
Item 2 is totally doable.
Item 3 already exists in the form of http://usestrict.net/2012/12/handling-fee-add-on-for-eshop-shipping-extension/
As for changing the UPS label (or doing number 3 without the handling fee add-on), you can always do what I said and modify the XML returned by UPS using the appropriate filter.