From a friend of mine that does lots of rally work: "What big race are you trying to win?" That extra 4 lbs of weight will be relatively insignificant. The 2013+ Tauruses are heavier than the 10-12, so the difference in time may be attributed to that. Also, are the cars you speak of the same? PP vs Non-PP? Gearing is different between the 2.
You may get the same initial bite, but the heat capacity is the main reason for going with the larger/heavier rotor. Ford purposely went with a much thicker rotor to increase the thermal mass.
As for which mod to do first: If you are ok with the feel, I would simply change out to the 13+ Rotors/Calipers/Pads. Maybe add in the Goodridge braided stainless brake lines. If you are starting from scratch and still have enough brake from the original pads/rotors, I would switch the master cylinder first. Or, just do it all at the same time...only have to bleed the brakes once.
Something to consider with the earlier brakes: The 10-12 use phenolic (plastic) pistons, so if you are putting a lot of heat into the brakes, they may distort/expand and cause some problems. I know on most AL calipers with these pistons, nearly every year or two, they have needed to be replaced due to this. The pistons on the 2013+ are Metal (Chrome plated Steel I believe) and are the same dimensions as the earlier ones, so they are an option if you are rebuilding your brakes. I have my full 2011 PP setup stripped and plated in preparation for that rebuild, but I obviously did the 13+.