Whole map versus Room-by-room? [Design Conundrums]

[nijineko 3]

My current project is to recreate an homage version of a very old ASCII rogue-like as a mobile game. The maps from this game consists of walls, doors, secret doors, and openings. The maps also featured one-time fog of war (once explored, always revealed). In rooms, one could find things like stairs, traps (pits, shafts, energy, teleport, guaranteed monster encounters), and various magical effects (darkness, anti-magic, illusions). Based on the combination of these things, one could also find hallways and large rooms. 

I have started creating a whole map for this game, only to find myself asking some questions. Here is a list:
 

1. Should I design a whole map, or create a unit by unit map (where a unit = rooms and hallways).
2. If I choose unit-by-unit, can I reuse these rooms yet still keep track of where they are in the big-picture map?
3. If I choose unit-by-unit, can I add and remove unique features via some method (global events?) to prevent visual repetition?
4. How can I best emulate the special features of traps and magical effects on the map level?
5. How should I best pull off the fog-of-war (any good plugins out there that are play-tested and recommended?)
6. How can I include a "create-your-own-character" mechanism in the game? (Both visually and mechanically)
7. How can I include mini-games?
8. How can I include crafting?

Today's post focuses on questions 1, 2, & 3 only. Future posts will cover other questions. 

What experiences and suggestions does everyone have in this area? I'm looking for opinions, ideas, and brainstorming; though if you have technical details of how-to, while that is most welcome, it is not expected at this point.