i believe you can program up to 4.. i have 3 on mine right now
the tweeter screw covers.. good luck finding them! mine have been gone for quite some time, pretty sure the only way to replace them is buy the whole tweeter pod assembly.. you cant even see it when the doors are closed
the hood prop clip you can get off of any Isuzu.. mine broke 3 years ago.. never bothered fixing it, the prop doesnt go anywhere
our rear view mirror is pretty standard, i think older model sunfires (97ish) use the same mirror as us, so most pontiacs/GMs probably do as well. find one in a part yard, clip the plug off and splice in a new one, from the look of it you can probably fix yours, just take it apart (the gray piece comes out and the wires will release) cut the wires, you may need to get the wire ends, you can get them at pepboys, and put it back together
i think one or two others have had headlights damaged from transportation, there are good writeups on refinishing the headlights, just search
as far as i know, no options for a flip key with compatible remote.. im sure if you are willing to spend enough money you can find SOMEONE to make/program one
the D indicator light sounds like its probably just a bulb, the dash comes out easily with 7 screws and then the gauge cluster with another 4.. pretty easy to take out if you are a do-it-yourself kinda person, i dont remember off hand what size those bulbs are, i would guess probably a 74, or plastic screw in style. if you cant find the bulb, just take it out of your 2 or L.. most owners never use those gears anyway (except for me!)
I dont know if the JDM VXs came with auto climate control.. you may just need to get small stickers made/cut for that