Chrysler Repair: Electrical, chrysler lebaron convertible, 1995 chrysler lebaron convertible

Question
Have a 1995 Chrysler Lebaron Convertible. 3.o V6.
The check engine light came on and the oil meter was low so i decided to stop at jiffy lube. They put in the oil then said that the battery was decharging. We decided to take the car to a family mechanic. We charged the battery with my uncles vehicle. The battery was charged until we thought it was long enough. Started the car and it started then we shut it off and then we noticed the hazards were flashing, along with the back brake lights. The hazard button wasnt on. Tried to start the car again but wouldn't run. It started but after about 5-10 seconds it would die. Bought a new alternator but it still does the hazard light thing and wont run. What is the problem. We have left the battery cables off until we find out the problem because it still does that with the hazard lights. Thanks.
ANY ADVICE WOULD BE HELPFUL. Have had the top fixed and a new transmission and have fixed the oil and radiator leaks.

Answer
Hi Will,
If you still are having trouble getting the engine to run, the most useful thing to do would be to try to get the fault codes that may stored in the engine controller memory to readout. Try using the ignition key: turn it "on-off-on-off-on" and leave it "on" (doing this quickly, no longer than 5 seconds). By "on" I mean just the normal position when the engine is running, not the cranking position. The 'check engine'light will remain on when you leave the key in the "on" position with the engine still not running. But then watch the 'check engine' light to begin flashing, then pause, flashing, pause, etc. Count the number of flashes before each pause and keep track of the numbers. Repeat the readout and verify the counts are correct. Then group them in pairs in the order that they came out, thus forming two digit numbers. You may notice that the pause is shorter between the digits of a given number, and longer between the numbers themselves. Then send me a 'follow-up' question telling me the results of your readout. By the way, 55 will be the last number (two groups of 5 flashes each) and that is the code for "end of readout".
I have the troubleshooting manual for the 3.0L engine and we can look up the possibilities of what is wrong based upon what fault codes you show. There is also an essay on fault codes at the site:
http://www.allpar.com/fix/codes.html
which gives the meaning of the code numbers. But then you need to get specific info for what exactly might be the diagnostic tests or parts to replace to complete the repair.
On the light problem, I would suggest that you take a look at the body computer which is located above the passenger side kick panel (to the right of the passenger right shin). Unmount it from the cowl and then remove the two 25-pin plugs and inspect them and their sockets for water or debris that might have dripped down on them from the windshield above. Use a spray contact cleaner from an electronic supply store to remove any crud that you find and to dry up any water in the sockets. When water gets on the computer plugs some strange gremlins are unleashed in the electical system.
Finally if that does resolve that issue let me know and I can tell you how to test the multifunction switch at the dash to see if the problem might be at the hazard switch itself. Also when you say the brake lights are flashing do you mean as if they were also a part of the haszard flashing system. It may well be that they are and what you see is normal except that you haven't asked the car to do that. So please clarify that issue for me as to which bulb are flashing.
Roland