I have a 2007 Mercury Milan. I had a remote start put on the vehicle, and the trouble I am having is that when the car sits overnight and I use the remote start in the morning, the heat shuts off. The only time this happens is when the car sits overnight. I have read some forums on the same problem happening with the Ford Fusions and I was wondering if you have heard about this.
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Should be part of fuel pump assembly. I looked at an online partsbook for your vehicle--2.5L engine--didn't show fuel filter. That usually means, the filter is part of fuel pump assemble.
Have you checked for applicable trouble codes? Your saying it stalls every couple of miles?
This car has one inline fuel filter, it is located under the car at the right rear, if you lay in front of right rear tire (passenger side) and look under the vehicle you might see it. You need a special tool to release the line. Any auto parts store will have the tools needed.
What brand is the remote start, and is it new to the vehicle or has it been on and working properly for a while?
Most remote starts have a feature that will shut the vehicle off when the brake is applied after the vehicle was started with the remote and the key has not been used to turn the ignition. However this is not what happened in your case. Some remote starts have an on/off switch that is installed under the dash, depending on brand and installation. If you have that switch, turn it off. If this does not correct the problem, locate the power with for the remote start and disconnect it. If this still doesn't correct the problem then is sounds like it has caused other electrical issues.
Was the new battery charged? If the new battery worked for a few days it is possible the alternator is bad and it is not charging the new battery. Start the vehicle and measure the voltage at the battery, it should be somewhere between 14 and 14.5 volts with the engine running. If less than 12.5 volts I would suspect the alternator and remove it and have it tested at a local parts store, This is usually a free service. Also could be a wiring problem or dirty battery cables.
A 2007 Milan might be still under warranty if it has less than 36,000 miles on it. If under 36,000 miles take it to the dealer for possible warranty repair.
Remove the lugs at the battery. Clean the posts and the lugs - then reconnect. Your battery won't charge (and the jumpers won't work) largely because of a film on the + post and lug. If you live in a hot summer area, (Arizona) the problem is especially troublesome.