One plug feeding both sets of wires. I don't see why it would matter if they were wired together as long as the circuit can hold the pull.
I run the Battery Tender 800 on my truck.
Waterproof 800 International - Automotive - Batterytender.com
Research "inductive heating". AND find another LARGER dealership. The orginal reflash would cycle the spool valves (or whatever) to prevent the injectors from sticking. LAst I have read Ford is now two flash strategies past the type you describe.
I doubt the harness will be there but you might find one that will work just from plugging it into the fuse panel.
Anything can be done given the time and money to do so.
I go to some larger tires first to see if the lower gears will do what you want. If you find you hate the new gears it's going to be expensive to go back.
My EGR experience says there is some sort of feedback by the EGR valve. My '04 would not throw any codes or CEL when the EGR valve was unplugged. When I modded my '06 up-pipe within the first minute of starting the truck the CEL popped up with a code for "Low EGR flow". It's a known fact that...
I've run a modded up-pipe that prevents exhaust flow into the EGR cooler thus the EGR system. My SCT is tuned to limit the EGR valve function to prevent a CEL or code. It works better than using Sex Panther!!
If you increase anything with the turbo you will need more than just an exhaust and intake.
All the previous posts are great info. Stay stock on the air intake, go with an MBRP exhaust. You could swap in an intercooler and a Accufab power elbow.