p3lon

i noticed in my car that some times it runs strong when i hit the full throttle and some times it runs slow. no pull when it down shifts. i also noticed in my exhaust does make a different noise. like is heavy and sometimes light. when it sounds light it ready to run.when it sounds deep/heavy it runs slow. so i am thinking is the tranny or engine. but it runs smooth. when i shift down to D. it shift hard.
Is a 94 sc400 with 250000 miles dont know if the original engine. i have a receipt of the tranny. it was install in december. i only had the car for a little bit over a month. i did a full service plugs change the fluids on tranny and engine. added a tranny coolers. some times i get a check engines when i am driving fast but turns off after i slow down. i did a smoke test about 2 weeks ago and it past.