Just to answer a few of your questions...
About the gt40 shaft... the gt40 and gt37 shaft are in fact the same size. But the turbine heads are different.
About the .72ar cover. As far as I know in the 6.0 world... only Elite and KC turbos use that style cover. It is used for many reasons. One is the higher flowing CFM. Two is the fact that the cover looks better (IMO
). Three is that the cover is physically smaller in size so it fits much nicer. Four (depending on the company)... using one of these covers means that you have a CNC factory made compound radius curve which is precise and produces very consistent results. Many turbo builders just use a lathe to cut that compound radius curve by hand which can lead to inconsistent results.
MTW used to make a stage 2 back in the day that used the gt40 cover. It had really good results but was very expensive to build. MTW had to literally pay $1100 to buy a gt4088 turbo just to use the .72ar gt40 cover and backing plate. Because of cost MTW started using the standard .58ar stock compressor covers with all the other specs EXACTLY the same as the Original MTW stage 2. That turbo was called the "hybrid" which ended up being a total flop and most people had major problems with it... only difference was the .58ar cover and .72ar cover.
I also know people who were having surging issues, stall issues, low boost issues, high egts
, etc... they switched to a .72ar cover and all the issues went away.
I also know people who had nothing wrong with their turbos, but switched to a .72ar cover and loved it.
... is it worth it??? Maybe... but if you just got your turbo built by James then I would run it and see how it does. James is known to build great products and I have heard very few issues with anything that he builds. I would give the turbo a shot and see how you like it before jumping onto anything different.
Just for reference. Here are the turbos that I was talking about...
Elite's powermax HO turbo uses a gt40 style cover
www.elitedieselengineering.com - PowermaxHO
KC Turbos stage 1.5, stage 2, and stage 3 all use the gt40 style cover. They dont have a website but WPE does sell their turbos
KC Turbos - Ford 6.0L Powerstroke Stage 3.0 Turbocharger - Turbos