What is wrong with my 1987 Prelude?

It kinda sounds like the same issue as Phil S had with his Prelude. It idles fine, but when I go to accelerate it kinds cuts out some until I get the rpm's up. Now, I've had this car 4 years. It ran fine until I let a kid drive it & he blew up the motor. My brother's INSISTED that it was the transmission so deferring to their expertise (although I knew it was the motor) we changed that THEN got a motor (took two years to get it all back together). Now it's not "right". I KNOW my car, it used to run tight & sweet as a dream & there is definitely something wrong. I just can't pinpoint the problem. Of course I will have the vacuum lines checked, but is there anything else that would cause this? BTW, they DIDN'T drain the gas, so I had to put fuel cleaner in it & run it out then replaced it with fresh gas. It helped my idle problem, but I still have the other cutting-out problem?