I've replaced the plugs with GM plugs, I've had the ignition coil cleaned off, replaced the fuel filter and put Borg Warner wires on and it's still missing. Could it be the wires that are still causing it to miss because they weren't a GM item?

Check/tighten your intake manifold bolts

Did you try the EGR valve?

Welcome to the 96 Eldorado misfire club. Mine has had an intermittent misfire for some time now and I have tried about everything. Doesn't miss all the time but it's a pain when it decides to start doing it. Good Luck!

I have heard others say they have had problems with aftermarket wires an to stick with OEM. When my car developed a mis after the fuel rail replacement I put new OEM wires on it. Problem solved.