2000 Lincoln Town Car Questions

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Seems to only happen while going 35-45 mph. The car has a slight pulse every few seconds. Doesn't seem to happen at all whole accelerating or idling
I have a 2000 Lincoln town car executive series 4.6 v8
Alarm Is triggered can't car cranks but doesnt start
I have a 2000 Lincoln Town Car, it has 160,000 miles, about 5 years ago I changed the intake manifold which is made of plastic, no I am having the same problem and I want to know if the Professional Products intake manifold 54060 which is made of aluminum, is this the best option, because the other are made of plastic. Thank you.
The rear of my town car does not lift at all, compressor runs, i rrplaced air bags and solenoids and checked airline and no leaks noted. Please advice
My car idles high at startup and won't hardly idle down to put into gear. When I can put into gear, it accelerates on it's own I don't have to push the gas pedal

loose, don't go in park
If I maintain accelaration through the next gear I can throttle down without it losing all throttle. And when it does lose throttle to regain it all I have to do is slow down to first gear and it regains throttle again. Also there seems to be an abnormal amount of warm air coming through the defrost vents that leaves a film on the windshield inside the car. I checked the code the service engine light was kicking back and it was P0401 and piston #2 & #5 misfires. I replaced the EGR Valve but nothing changed for the better or worse.
None of my windows work except for the front passenger.
Car Wont go into third gear seems ike it looses pressure but won't cut off
Put charger on it will start for a few days, then clicks. Last time it started, a few minutes later started clicking. Have been told the alternator is ok. Is it the starter? what does it cost to replace. When it clicks put charger on it and it always starts.
All of my window work, using the power switches including the drivers side switch. But my drivers side window want go up or down using the switch.
The car front end sits low and leans to the right. Whats wrong
I thought it was out of power steering fluid but it'd not and it's a loud sqieeking noise when I turn the wheel back and forth
There is a small motor running on the driver's side under the hood. It is enclosed. This motor turns on and off intermittently. Even when the car is not running. I know it's not my fan. I don't know what it is for.. The box it is in is part of the car. I can't see it but it is kind of loud.
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