2006 Mercury Milan Questions

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battery light stays on even when car is running. Alternator was replaced. Battery is good, but battery light still on. What should I do
clutch went out the mechanic says its the hydraulics
I put a new battery in and I start my car and it says my charging systems good but when I turn my car off and turned just the key on it says check charging system is that supposed to do that
happens after short period of driving, when climbing hills, or after sudden stop
car runs fine just stop going in gear
a message also came up saying to check charging system. I noticed the radiator fan was also running . What has happened?
Im not exactly sure if a wiring harness was used or if wires were spliced when avi installed my radio but i paid for the harness. Is it possible that. This new radio can cause the PCM to go out, problems with the A/C and cause a short in interior lighting?About a month after installing the new radio not only did my AC start acting up but, i was driving down the highway and all of a sudden my car just went out on me. Error is all that would appear on my dash. We tried unplugging battery and a bunch of other things. I hooked my car up to a computer and the code u0100 appeared, meaning loss communication with pcm. We tried reprogramming the keys almost three times but it would run for a bit then the same problem occured. Ford diagnosed the problem and I had to completely replace my pcm. Also my car started running hot and my blower motor relay went bad, which i had to replace and now my car blows air when it wants and normally just hot air. My AC can be on off but it will randomly turn on and off. Can installing this radio cause all these problems because my car was a very good reliable car before changing the radio. Once it was changed its been problem after problem. I also believe it may have a short in my interior lighting because the right light above my dash flickers the whole time when its on. Once the radio was installed they did inform me that my steering wheel controls would no longer work but i didnt expect all this.
When driving and it gets to 3rd gear it doesn't want to shift I have to take my foot off the gas and sometimes throw in neutral for it to go back into the drive like I am forcing it to shift it started at 80,000 miles and I have drove it 156148 miles so far but I am afraid it's going to cause me to get in a wreck on the highway when I try to speed up and it feels like it's just a neutral. what would cause this?
I press clutch pedal in to start car and pedal doesn't spring back up
what should i do how do i fix this problem
I start up the car and put brake on but it won't let me push in button to get i n reverse or drive. if I use a pen in the little hole next to shifter it will then ingage
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