cougars dead again

[romntictragedy]

i had a new alternator installed (self exciting because they couldnt get a regular one to respond in the car) in October ran the car maybe 2 days and parked it to move to cali. for the winter. i started driving it again recently and noticed my gauges were flickering and my battery wouldnt hold a charge overnight. I had everything checked and it tested good. So i figured start looking at short wires but still had a feeling it was a battery/alt. problem. well being stupid i took the battery out while the car was running to check to see if my gauges were working and it was infact a dead battery. smoke started rolling outa my dash and the car bogged out and died of course because it shorts the car out(didnt know that at the time) well it was my illumination wires. Fixed them no shorts in the harness other than that. Car still wont start. I have spark to my plugs. No fuel pressure but can here the pump kick on as soon as the keys on. checked my diagnostics the only thing i got was low battery voltage from that. the battery was brand new and pre-charged when this was done. Have checked all fuses and as much of the wiring in the motor as i can see. Any clues on what this could be or what to look at.