Let me address just one of the issues and clear that up first before tackling the others.

I made a test transaction on your site (picture attached) and I see USPS Parcel has a lower rate than USPS Priority, not the other way around.

Disable all quote methods other than USPS and turn on the quote debug display at admin/store/settings/quotes/edit. Then you will be able to see the response from the USPS rate server, which contains all the services and rates that the USPS server is returning to Ubercart.

You can determine the exact USPS rates to expect by going to http://ircalc.usps.gov/ and entering the appropriate information. I can't tell what the store ZIP is so I can't compare the quote I get from your site to the one the USPS tell me. From your test site, I get quoted rates that are much higher in all respects than I would expect, so I assume you're applying a rate markup. I would turn all adjustments off so you can compare the quote determined by Ubercart with the quote from the USPS web calculator.

If you can give some specifics about a particular quote you think is wrong (source and destination ZIP, package weight, complete output of the debug messages you turned on above) it should be easy to verify whether the USPS server is returning the wrong information or whether the shipping module is processing that information wrong.

I have run many test on the USPS quotes as I've set up my store. I have a set of actual orders from my old site which I've entered into my new Ubercart site - I use these as tests to compare the USPS shipping cost charged to the shipping cost I actually paid for that order. (This tests not only the rate quotes but also my product weights and assumed packaging weights, and lets me fine tune my markup to cover my shiping costs.)

I have not found any difference between what the USPS server returns and what I actually paid for a specific package.