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Common leak areas are windshield seals on many cars. Most of the time testing starts by having someone inside the car inspecting possible trouble areas, while an assistant sprays water on the outside of the car. The drains for the cowling are external of the cab, water would be pooled very high in the cowl if it is blocked up, and from there likely enter the HVAC plenum and either simply go out the AC drain, or end up on the passengers side floor. There is another trick that can be used, with the blower on high and drawing outside air (not recirculate) close the car doors and windows and use smoke to find where the air leaks out of the interior.
There are a number of ways to reset the system. First turn it off in the trunk, then turn the key on, and then turn the system back on. Get into the car, shift to drive while holding the brake. Now shift to park, and unlock the doors and get out of the car. With the drivers door open, go around the car and open the passengers door and then close it. If at any point you hear the compressor come on then the system is operating and the light should go out. Otherwise you may need to check with a shop that has the Ford NGS or IDS scan tools to see if there is a problem.
The module shouldn't fail because of an incorrect key, it just shuts itself down for a period of time. Wait two hours, use the correct key and try to start the car. If it doesn't start, just leave the key on for three minutes and then try. If that doesn't work, then maybe the lock cylinder wires have failed (very common problem). There are work-arounds for this system to get you by until you can have it repaired.
Where is the 3500 number coming from? When it comes to completing monitors the first trick is to look-up the codes that the monitor could generate and study the code enable criteria. That will give you the exact conditons that have to be met for a given test to run. Ford is very strict about it's routine, the O2 heaters must complete before the O2 sensors themselves are tested, and the Catalyst monitor doesn't run until after the fuel trim and O2 sensors have been tested. So, something is blocking the O2 heater monitors (tests) from running, and what ever it is will be spelled out in the code enable criteria. There are lots of top techs who can handle this repair, and they don't all work at dealerships. One out of five cars that I work on are sent to me by other shops for just this kind of a problem.
First thought is secondary ignition insulation is weak and allowing the spark to jump out, instead of across the gap of the plug in the cylinder. I saw your other post, and you already replaced the catalysts. You need to fix this misfire or you will destroy your new cats. At the least if this is a misfire you need to replace the plugs and plug boots. If there are any bad coils, replace them, putting the new in the rear head if you are only doing some of them. It's a good strategy to replace all of the coils if you choose to because a bad coil can take out it's driver in the PCM.
What engine? The 2.0I presume? The right way to do it is with the tools to hold the camshafts and the crank shaft in place, and the belt gets installed with the pulleys loose on the camshafts. It's not too bad to do for an experienced person. The 3.0 uses chains and guides, no idler pulleys.
If there is you should find a lever to control it and it's operation would be noted in your owners manual. Does your SantaFe have a dual climate control system? Restrictions in the heater cores on some cars can result in some unequal heat distribution.
Have the car tested for a dain on the battery, and don't be surprised if the radio ends up being the drain should it have one. When those radios fail we send them in to a Ford Authorized repair shop, and they will take it apart and return the CD's. That's the best way to do this because the radio has other vehicle responsiblities that aftermarket units can't do.
Nothing abnormal about needing brakes. Everyone uses their car differently, so the intervals are different, but needing pads and rotors is normal with many cars here in the rust belt. I can't say what happened in AZ since wouldn't expect to see the corrosion there that we get here.
The smoking could be some of the oil hitting the exhaust, which could ignite it. If that happens the car could be badly damaged or destroyed by a fire. Have it repaired immeadiately.