Still runs bad after tune up

I have a 93 LX, 5.0, 5 speed. I just completed a tune up at 110,000 miles. The engine hasn't run right since I had the trans out about a month ago. I'm getting a check engine light and the code references the egr and O2 sensors. The tune up consisted of, oil change, msd cap and rotor, Ford Racing 9mm wires, NGK plugs (gapped .045"), and an MSD Blaster TFI? coil. It seems to be running okay but I am still getting the engine light (yes I did clear the code). This is what it is doing, kind of stutters (best description i can come up with) for a second on start up, it seems to be down on power when I accelerate until a certain point and it really takes off all of a suden, and every once in a while when I first start driving it will backfire. I have yet to check the timing and I just switched from 89 to 87 octane fuel. I think I have listed everything. Let me know if you have any ideas.

Smitty

donkey_punch said:

so how about changing the EGR and the O2 sensors? there a reason why it came up in the codes. cause it needs to be replaced. clearing the codes does not clear the problem. and the O2 sensors and egr are not that much money also.

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No $hiT on the codes. I know clearing them doesn't get rid of the problem. One of the two (O2s of egr) can cause the other to throw a code. I just don't know which one and why. When I had the tranny out I had to unscrew the O2 sensors. I wasn't rough with them but I did wind the wires up a little. Didn't want to detach at the clip because they did not want to come off easy. Think maybe they could have been damaged anyway? It just seemed weird that all of a sudden it runs like $h!T and I didn't even touch the engine.