skoda laura problems after ecm change

hi all

i am having a hard time with my skoda laura automatic diesel car, a few weeks ago i was driving back home from work and i took a halt for about half an hour to have dinner, later when i tried to start the car the engine would not crank at all and all the dispay lights around my speedometer would go off as soon i as turn the key to ignition. i could operate my window glass, sunroof but the car would bot start. i called up my mechanic and asked him to come and have a check. when we openes the hood there were papers and plastic bags which indicated that the rats often paid visit to my car. after checking my mechanic said the rats have cut the wires. and he would have to take the car to the garage. the next day he called up saying that the wire cuts have caused short circuit and has damaged the ecm which wil have to be replaced. i agreed to a used ecm for about $ 300 (20k INR). he also said that the baterry has also gone bad cause of the short circuit so wud have to change that too. after about 4 to 5 days when i got the car. it wud start fine but all the warnig lights for esp, abs, ecl, wud come on, now when i went fthe test drive i cud hear a lot of hissing when i press gas, i had whistling from my turbo earlier but not hissing, this hissing sound is very loud. secondly it initially gets stuck on the 2nd gear and goes upto 350 rpm but doesnt shift to the 3rd. when pressing gas a little more it actually looses accelrartion and causes jerks and makes noise like a bad motor ( i dont know gow to describe it the best) i have to press gas very softly in order to make the car move this goes on for a few kms and than it wrks fine. i have lost the pick up which i had before the ecm change. i am wondering what wud be the prob here ? is it a vaccum leak? a boost leak ? which is causing the hissing and pick up issues? or is it the ecm? i m not sure what is causing the gears to not shift correctly initially dor a few kms. i can also see white smoke when the car jerks. 

i have zero knowledge about cars please bear with me and guide me in laymans language.