Could not get the PCM to communicate

Electrical problem 4 cyl Two Wheel Drive Automatic 80,000 miles

I have an 03 Pt Cruiser with almost 80,000 miles on it and its really not making any sense to me. The history on the car is as follows: At 77,000 miles we had the fluids changed, which included the transmission fluid being flushed, two weeks later my entire transmission failed. It sat for a number of months outside before sitting again at Chrysler. Chrysler said they could not get the PCM to communicate, so they replaced it and said it still would not communicate. We went to Amco who said the battery was to dead to communicate with the PMC. They totaly rebuilt the transmission and I replaced the battery. I also appearntly blew (while the car was dead) and had to replace fuse #18 (20amp, yellow) in the Power Distribution Center box under the hood. It's used to control Ignition-Off Draw = IOD. The owners' manual explains that it's used to keep the battery from draining during extended storage. The Car ran fine for a few months but all of a sudden it started running hot when in park, I added coolant and it seemed to stop. Then a strange noise, like a gurgling, would sound from under the car when I would accelerate quickly from a stop, but only for a second. The final straw was when in park and idleing there would be a buzzing sound that lasts a second or two and from under the hood a poof of steam or a wisk of smoke would come out, its hard to tell which. I took to firestone who previously, right after the transmission problem, said I had a coolant leak and that my water pump was about to go, thinking that this could be the problem. I get a call from them that that the car is inside their garage and it wont crank. They also tell me that the check engine light came on while the car could still turn on, which had never happened for me, and said they pulled the Codes:
P1681-Malfuntion Control Output Circuit
P1604 - Same Message
P0462- Fuel Lever Sensor Low Voltage
P0340- Cam Position Sensor Circuit
P0335- Crankshaft Position Sensor Maulfuntion A

The Firestone people didnt know anything about anything. They blamed the computers in the car. I got a call the next day, they say now it starts and I drove it home and it drives fine, but the engine light is still on. I dont know what to do, is it worth saving this car, is the pcm bad(even though I just replaced it)?