the last time i went to the US, i drove an explorer from LA to vegas. okay naman. i'm guessing its the streets here in manila that's causing undue and excessive wear and tear on the vehicle. that being said, for a 2.2M vehicle, that really sucks.
if you ask me, your explorer looks like its okay. no major mechanical problems so far. what i'd do if i was in your position: forget the casa (they aren't doing a good job anyway) and bring your explorer to your trusted shops instead. for the aircon, i once had this problem with my honda civic. i brought it to an aircon place and they traced the problem to an incomplete closing of the outside vent. they fixed it and haven't had any problems from the aircon since.
for the rattling interior trims, bring it to an interior/upholstery place. let them dismantle the interior and apply foam insulation. that should do the trick.
while its bad that you got shortchanged with this purchase, i think you can make the most of it by having the problems fixed. i know that sucks pero i cannot fathom losing P1M in just two years (if you sell the car now). personally, i'd salvage the car by fixing the problem and sell the car after about 5 years. by then, the resale value shouldn't have depreciated much from today (it seems to me that the resale value has already depreciated to its lowest value and shouldn't go down much anymore). sayang kasi and besides, the explorer does look nice.