Dan,
you do have a nice and extensive kit and it seems that you got many angles covered. But until you put it together and start carrying it there is no way of knowing how it is going to function. Many guys here started with heavy loads and by honing their skills realized that some items in their kits can be left behind.

Just few suggestions:

Good pocket knife (Sebenza, Buck, Ritter Knife are all good choices...) Get a knife that doesn't look too military and is not that expensive. Maybe even go for one of the swiss army one hand opener locking blades they have out there. But Ritter Knife seems like a good balance and good value for the buck. Why not expensive even thou you may want to own a nice knife? Things get lost in the city, there is always that one dumb cop that can take liking to your knife or you may need to secure your blade with a guard and not get back what you stored.

Carrying extra items seems to be one of the bigger problems for all of us since we don't really want to attract attention. The most common practice I have seen are modular kits with items sorted by frequency of use or priority all put into one case that can be slipped in and out of the main pack. I prefer personally my Acteryx sports pack or my Alice pack (small one). Latter has a militay look but it is not too hardcore looking like BlackHawk or Maxpedition (sp).

Extra clothing is good but in the winter time fleece and maybe some rain gear should be sufficient. I carry a rain jacket no matter what but I ditched my rain pants. I would throw an extra fleece sometime but more than often it's other people who wear it. I carry the nissan thermos with some earl grey tea if I know I will be outside in the winter for a long time (such as trying to hit on girls in the park while walking my dog)

Needle nose pliers (bec the champ's pliers suck.I see a leatherman in my future) - Yup buy once and buy good. I was a Gerber fan and I switched to Leatherman @ 2000. Never looked back.

Exacto Knife with spare blades - WHY?

Hammer (small wooden handle, not very strong but lightweight) - WHY?

*Pry bar (small to medium in size) - WHY?

Those three items if found on you will clasiffy you as possible bulglar

*Glass punch

*N95's or N100's with locker

*Bandana

*Evacu8

*Goggles

*Leather gloves You may want to get the fire resistant leather gloves from GALLS and kill two birds with one stone

*SureFire E2E (spare lamb, batts, batt case) - don't forget extra food for the lamb, is there an LED lamp assembly for that light? You may want to get it due to longer battery life and bulb life.

Photon light attached to the inside of carry case with nylon line and quick release

Chem light (and holder) - Chem sticks have a tendency to activate themselves if carried in bags. Ditch the holder. You got duct tape and paracord.

*spare batt for CMG infinty

Map of the NYC subway system

Map of NYC

Compass (silva type 7, I have a ranger but don't want to risk huring it in day to day)

*AM / FM radio (with batts, if money allows maybe one that is also a scanner)

Whistle (Storm)

Para cord (50'' )

Duct Tape (flat)

Mini bungie cords (2 red)

Cable ties (15 large)

Brass wire

Emgergency Space bag

Sharpies (one regular and one large)

Note pad (in plastic map case) -

Pen (bic)

Waterproof Matches in hard orange case with striker attached

Candle

*Eye glass repair kit

*Spare glasses in hard case

*Biner (I like the locking kind)

*Cash (at least $150, maybe 50 in ones and the rest in 10's)

Quarters in a film canister

*Metro card (subway and buss card to all those non-New Yorkers among us)

*Calling card (need to do research, I think someone posted about this b4)

*Contact Numbers and other important info Put ICE (in case of emergency) in your cellphoen for emergency workers...

*Spare house keys

Power bars [2]

32 oz Nalgene with water

Gookinaid

*Gerber milk bags [2]

*MP1 tabs

*Pottasium Iodite

*Door Stop Wedge (got the idea from another forum, enables one to check an escape route while still retaining ability to back trace your steps through a door) - Good idea but you only have one. Fire teams when securing their escape routes have many of these at hand. If you really want one there is a special fire man tool (http://www.thefirestore.com/store/product.cfm?pID=740)

Bug spray

Sunblock lotion

Altoids Tin:
-mini bic
-twisty ties
-second photon light with clothing clip
-small roll of dental floss
-saftey pins
-sewing kit (small hotel style)
-couple of paper clips
-couple of rubber bands

FAK (this fits inside the soft case. I should note that this is a EDC FAK and not my "home FAK", which is of course much larger and more thorough)
-bandaids (regular)
-bandaids (extra large)
-rolled gauze
-2x2
-4x4
-moal foam
-moal skin
-imodium
-advil
-tylenol
-neosporin
-gloves (non latex)
-CPR mask* Are you CPR certified?
-eye wash*
-emt shears Get a rescue knife from Spyderco with window punch and whistle, about $50 but you will save on space and quality is much better than shears)
-antacid
-benadril
-tweezers
-medical tape

Items I have thought about but have not added to my list (yet ).

-Small binoculars
-Poncho
-Hack saw blade
-Electrical tape
-Wetwipes
-Ranger Band
-Water filter
-Sewing kit (larger)
-Rite in rain paper and pen
-Brunton Helios lighter - hard to justify an expensive lighter in the city, but might get it anyway, bec its cool. It is cool but as a person who loved his windmil I recently went back to Zippo. Routine maintanace forces me to make sure that my ligther is operational all the time
-MRE (one meal) Also get a heater. Carrying a spare meal is always a great idea.
-Israeli Trama bandage
-Quick clot
-Spare ATM card?

I hope that you do understand that you are talking a lot of gear here. (Who am I to even say that). But you have items there that are heavy and really questionable if you are ever stopped. I have no idea Dan what you do for a living, how old are you or how you look like but the sad reality is that every one is profiling out there. You have all that stuff on you and you fall under a category that somebody doesnt like you will have some explanations to do. Are you doing something illegal? Absolutely not but it's a waste of your time which I'm sure is pretty valuable to you. Also in case of NBC attack if FDNY executes their full decon plan you are loosing everyting you carry. Also heavy pack slows you down. Also even if you can justify the possibility of carrying all gear probably the key will be organization. You have a lot of smaller misc items there that if thrown in without a plan will disapear and be impossible to find when needed.