#1. I have just done a complete uninstall of FSX/Acc and all FSDT.I need to know if I should leave the Registration Entries in C/USERS/NAME alone for the reinstall?
They will save for having to manually type your Serial Number in case you'll have to reactivate. That's their only purpose, losing them is not a problem (not that you'll gain anything by *removing* them either...), just that you'll have to manually type the Serial Number, instead of just double-click on them to have the Serial Number inserted in the registry without typing it.
None of this is needed anyway when reinstalling FSX or the sceneries. You need a reactivation ONLY when changing major hardware components or reinstalling Windows with a reformat of the hard drive.
#2. There is also a file in C/USERS/NAME/APPDATA/ROAMING that is titled Virtuali with Airplanes,GSX,Couatl.err,Couatl,Coutal addons and Key mapping.Should I leave this alone?
If you remove them, you'll lose all your customizations for airplanes (the "Airplanes" folder) and sceneries (the GSX folder) and the GSX preferences (the Couatladdons.ini). The Couatl.err and Couatl.log can be safely removed. Again, you will not gain much by removing them, other saving a few kb of hard drive space.
The main concept is: if there were files that SHOULD have been removed when reinstalling, we would obviously do it in the Uninstaller, which should ALWAYS used (and this is valid for ALL your other FSX add-ons, at least those that HAVE an Uninstaller) before uninstalling/reinstalling FSX itself.