The 1A,B is refereing to the drawings below the wiring diagram, your vehicle transponder connector should resemble either connector A or B in the drawings.
Key programmins 3 or 2 is giving you the option of programming with 2 keys or following the 1 key dcryptor method, both work simnply choose one and follow it.
https://fortin.ca/download/22301/evo-one_ig_reg_bi_for_b_22301.pdf
Yes Rx and Tx will need to be connected along with all other required connections such as ignition wires, brake wire, door lock wires, parking light wire etc.
There is no can bus in this vehicle hence why we say to activtae option 20.2 for tachless, Also we do not support 3x lock from the oem remote on this vehicle. As stated on the website you will require an RF kit.
https://fortin.ca/en/vehicles/mercury/milan/2010-standard-key/