I figured out my issue. It is that of reading instructions lol. From This post on the MKZ forum, i was supposed to plug in both the Bingfu antenna and the FAKRA antenna (original antenna) since the JL3T - 14G087 - CK TCU has two ports. I had only plugged in the Bingfu antenna 
After plugging in both antennas, i did a sync 3 master reset and used forscan to reset the TCU as mentioned in the linked post. After the reset, i think you don’t have to change the first line of the TCU on forscan to B132-XX from B142. However, i left mine to B132 as i had previously changed it already.
After TCU reset, i performed the service bulletin steps for valet mode on then off from Ford that is also linked from the MKZ forum above. Following all this, i downloaded the lincolnway app, logged in, added my vehicle and was able to activate it right away. No need to update TCU firmwares etc. I then stepped out, manually locked the car and tried all remote features. Everything works. Drove it tothe gas station to fill up my tank and vehicle page updated accordingly afterwards.
Moral of the post, take the time to read instructions carefully lol. This whole journey has been a learning experience and also showed me how not very helpful lincolnway support service was.