Hi Chihsin,
I live in NYC and care for more than a dozen Ficus lyratas and have for over 30 years. Humidity is not the problem, so you ca dispense with the pebble trays, humidifier and showers. When properly irrigated, Lyratas do just fine in low humidity. Likewise, stop fertilizing. Fertilizer is intended for healthy, vigorously growing plants that are using up nutrients in the soil. It is not medicine.
Light may be a problem because your windows are overlooking a courtyard and not receiving as much as a south or west window would in locations outside the city. Your Lyrata would benefit from a few hours of direct sun. Move your plant directly in front of a completely uncovered (no sheers) window.
Watering Lyratas is tricky. They do not tolerate dryness very well, but they also do not like constantly wet soil either. I suggest that you allow no more then the top inch of soil to dry in between thorough waterings. Develop a consistent watering routine.
In FL nurseries, Lyratas are grown in two basic forms - tree and bush. You have the latter but apparently prefer the former. The multiple stems is the tip-off to that. It will be very hard for you to achieve the tree form vision that you have. You can remove the lower leaves if you prefer, but having multiple bare stems at the bottom may look a little odd. But that is personal choice. Howeve you prune, it will not affect the health of growth of the plant. It will only alter its appearance
The important thing is to get the light and watering under control so that all future growth will come in healthy and blemish-free. Existing brown spots will never disappear, so it is important to prevent more in the future.
~Will
Q