you’re ahead of the curve here. I looked up MerchantShippingGroupName and familiarized myself with it. I looked up one of your $100+ items [ BAC00706 HO BNSF Rail Chief Freight Set by Bachmann ] and all appears to be correctly set up on our side. I then checked Amazon and as you say, the shipping template is set to Standard not Expedited as it should be.
I reset that item in the NitroSell WSM->Amazon->Reports tab and the product updated on Amazon. The shipping template for that item now reads Expedited on Amazon Seller Central.
At this point you have a choice to either go through the items you want to be expedited and reset them in the reports tab or alternatively, under the WSM->Amazon->Tools tab, there is a Reset All Items in Product Feed button. This will resend ALL your product descriptions to Amazon.
Whereas I am sure our side will work perfectly, you should be aware that changes could have been made to the Amazon catalogue since you successfully uploaded your products. These could result in you having to make changes to items that have been modified on Amazon. If this was the week after Christmas I would have pressed the button for you without hesitation. This side of Christmas I leave the choice up to you!