Kingdog,
The throttlebody gives you more air and the possibility for more fuel as the injectors are larger. If the heads have been modified they should accommodate the air that comes on the Screaming Eagle Throttle body
Something to consider is that the FLHX came with the 50mm throttle body just the smaller injector. On the 110's they came with a 46mm throttle body and the SEEGS came with a 43mm.
With the addition of the 50mm Throttlebody you can check with Harley, but I believe the spray is 4.89 gm/sec. So if you have some headwork done I would suspect you to see a gain in the 400 dollar expenditure.
The thinner head gasket if all things left alone would increase compression slightly but also has the effect of compacting the squish area for better performance. If the head builder was going to deck your heads ie take something off the face that touches the gasket and faces the cylinder he could just incorporate if you so desired that he didnt add any extra compression beyond what was already going ot be done there by say only taking off .038 instead of lets call it .040. While it is a minor compression addition, it can give you benefits and it would not be something I would be concerned with at all.