The T6XA will work fine. You may want to consider picking up a Matchbox r the similar product that Futaba sells to do the servo balancing. The Tx won't do it and a Wye is not the way to go for numerous reasons.

I suggest that you use new wiring in your plane. Anything that has been stressed over time by lots of use or a crash before is a high risk element for electrical noise or later failure. If those switches are new then use them. There is no real need for regulators on a nimh attery installation if you keep it either 4.8 or 6v. I strongly suggest the 6 volt.

The extensions require neither twisting or chokes. Just use good ones, such as Cermark.

Choke servo or optical kill if you feel that you need the shut off redundancy beyond the throttle trim or ignition switch. Either one would be fine but both is massive over kill. Use the lightest one.

Antenna routing is a matter of personal choice and a source of considerable arguement. I like mine outside the plane, others prefr inside. Tom runs his partly inside with part outside on the bottom. The method that provides reception without glitching is the one to go with for any given plane.

The best paint matching I have ever seen has always been done at an auto paint store. Very expensive but also very good.