2003 lincoln ls

Question

I have a 2003 lincoln ls 3.0 I was told it needed motor so I replaced it. It still runs the same the solenoids were shoeing up in the beginning and I had that fixed also now it's more motor codes like egr and 02 sensors I don't think these problems are big enough to stop the car. Well here's the way it runs it diesels and the idle is up and down it won't go up hills even in my yard I bought a new fuel pump that didn't fix it. And it's very loud by the air intake like it's ducking way too much air I use to could drive around town top speed 25-30 but now it won't even do that. It also has a catalytic converter smell but I had those checked twice!. This car puts and the mechanic I bring it to has sat around just guessing what it could be. I took it to Ford and they said they couldn't either connect to the computer or did this car have another pcm ever did? I don't know I bought it from an auction. And it also spark knocks also and the egr does make a knocking noise. But for awhile I've been worried is it a pcm problem I dont know. But every now and then it will jump to E-mode and then go back to drive or reverse. SORRY for so much info would like to figure it out very hood car besides that.