Yes, your list of actions should work. If you have something in your special email that already has a payment link, then you should be OK. Otherwise, as long as you set the order status to one of the ones that is set to show a pay button on the My Account page, you should be OK. There are only two built-in statuses that allow payment from the My Account page, which are “pending” and “failed”. So, if you are changing the status to the default “pending” status to edit the order, you could just leave it in that status, or switch it back to “wholesale pending” after you finish adding the shipping charges, and they would be able to pay via the My Account page.
Regarding #2 in your list, the next release of my plugin will set it so that “wholesale pending” orders can also be edited (so you won’t have to change back to regular “pending”). It may be a week or more before that version is released as I’m still working on modified functions and compatibility with the upcoming WooCommerce 3.0 release, which is the bulk of what my next updates will be handling.