95 4Runner loss of acceleration

Well about 4 weeks ago I cut the muffler on my 95 3.0 liter sr5 4wd 4runner. I ran a y pipe two 2 pipes out the back I still have my cats, but anyway I then changed the oil to a synthetic oil and it ran ok. Well I decided to go back to conventional about 900 miles later so I changed the filter and oil. Before this I have smelt sulfur, but anyways I started to lose acceration ALOT its to the point where I can floor it and its at a stedy slow pase, after 50 which will take Forever it regains speed and acceleration like it always had. I then checked the cats from one of the sides that was bolt on and saaw a nice yellow honey comb looking cat, so thats not the problem. It also runs bad when in drive, or reverse stopped. But in park or nuetral it runs great stopped I need help its olny got 80 thousand miles on it. Could cutting the muffler have done it, or a oxygen sensor or the fuel filter, My check engine light is on, please help me