fuel questions

i have a 97 gt. i just had a 99 cobra tranny put in. before i got the tranny back i had let it sit for 2 months on blocks . the day it comes back it want run right. i jumped in and took off 1st was great, second perfect, when i was hafe way through third the car felt like it died. Like it was starving for air or fuel. then I let off the gas hit it again itwent a little further and started dying again i let off and went to fourth and the car cut off.. im puzzled cause i drove it last night but i never went higher than 3000 RPM's in 3rd,4th,5th and it never cut off on me. Im wondering if when the guy put my tranny in could he have bent a fuel line? or maybe my fuel pump is going bad?, or maybe fuel filter, or injector.IDK but i need help and fast......... one more thing i noticed that the guy didnt install my shift boot correctly so of course i feel heat coming in but on each side of the shifter colom feels really warm kinda hot on your leg if your leg hits it. im talking about the whole thing from radio down to the shifter is warm.............. it really weird please help... if it helps the check engine light is own:shrug: