Hey XCali !
I missed this thread and first of all I just want to tell you that your city map is splendid.
Because of the large number of POI, putting numbers is the good choice, with only labels it would be too hard to find something on the map. For me, the labels are clear and easely readable, no need for banners. Now, from a player's or gm's perspective, to find a point quickly on a map it would be best if the numbers were ordered geographically. Most are, but some are isolated : I did a test with "42" and I spent a lot of time finding him because I immediately found the 43-49 pack and expected that 42 were nearby
There are some others, as 40-41, 90-91 or 60-61 for example. Separate the map into districts can be useful too. Of course this is not redhibitory and on the opposite placing totaly random numbers can be used for role playing : A GM can ask the players to go to some place and gives EXP/Bunnies/etc to the player who found the POI the first (or penalize her/him if her/his character is supposed to have a low INT/WIT/perception/etc.
)
Wait, I just realized that you have district names on your nightly map, why not have a map with district labels and POI numbers ?
For the pdf thing, I am not sure to understand completely but why not simply insert the maps as images in a word processor document and export it as a pdf ?