2000 Dodge Intrepid, alarm/remote start

There are two accessory wire. If you need the radio on during remote start. Power both the accessory wire up. Don't jump the wire add a relay instead. Try using a different value resistor for the door locks again. Try higher value. It's a very common issue with you vehicle. Which is why I only buy HONDA and TOYOTA vehicle. No relay and resistor require to get the keyless to work. Just a ground pulse will do. Be careful whose advice you buy, but be patient with those who supply it.

any ideas on why  the doors and windows don't work manually? are the linked to the acc wire?Don't get tired, get get better.

Do you mean the switches on the doors? Double check to see if everything is plug in and secure. Be careful whose advice you buy, but be patient with those who supply it.