Unique Overworld Boss (a la DoomGaze)/Creating New Area Question

Am I right in assuming that $CA/52D1:78 and $CA/52D3:78 have something to do with the invisible counter? I'm fairly sure they do, based on their physical closeness to the dialogue relating to the event, as well as their hex value of 78 (or 120 in decimal form, which is what the invisible counter starts at), but which one (or what OTHER byte, come to that) actually begins the countdown?

The code you are referring has nothing to do with a counter; it only makes the characters (Celes and cid, I suspect) to be able to go through objects, sort of like a "walk through walls" code. The 78 is the event command to allow specific characters to become "transparent".

Code:

CA/52D1: 78    Enable ability to pass through other objects for object $31 (Party Character 0)
CA/52D3: 78    Enable ability to pass through other objects for object $10 (NPC $10)

I found a timer that starts counting down the time, but I'm unsure what it is for now.

Code:

CA/5338: A0    Set timer 0 to $0040 [0m: 01s: 04j], jump to subroutine $CA533F if it expires. Flags:  
               (Countdown pauses in menu and battle)
               (Countdown not shown while walking)
               (Unknown flag 0x20 disabled on event bank byte)
               (Countdown does not override the game clock display)

The Cid actor which begins the event itself has an event number of 5370, so does this relate to $CA/5370:B2? Or am I making erroneous assumptions?

Yes, you are right. For some reasons, the event banks are given numbers (probably JCS can give you a more specific reason). Bank CA has a number of 00; bank CB has a number of 01, and so on.

The cid NPC's inside of his house in the WOR are associated with the event "5370" or, more accurately, 005370 (meaning you're referring to the CA bank, and can be translated to CA/5370). When the event is in the C2 bank, you will see a number 1 before the address of the event. Example, 1DD2E (means that you want the event at DD2E in bank CB, or more accurately, CB/DD2E).