Thanks for going through all of this and letting us know what you have discovered, this is very helpful. When it comes to the shipping type I was originally asking you to open the shipping quote server behavior on the confirm page, it is in this server behavior where the type is the first option. You can check it in this place if you need to update it again for some reason.
When it comes to the Payflow links please post back with what was present after you ran the wizard and what values you updated them to, I will use this info to ensure that this issue is properly logged and looked into. I will also do a test of the checkout wizard to see why it might be missing this value for the USPS quote. Thanks again for all of your effort.