Please Help!! Engine running rough/jerking/shuddering
 

So my '01 xlt 3.0 had a really bad shudder/vibration going on at around 50 mph and also when stopped at say, a stop light. Also had smoke coming from the exhaust at the first bend, underneath the oil pan and after the driver side manifold. Replaced the coil pack and the problem went away for awhile. Then a code p401, EGR flow blockage, popped up and the shudder and smoking pipe came back. So I replaced the plug wires, EGR valve, DPFE, and EGR solenoid. Shudder has gotten a little better but still there, especially when put into reverse or drive with foot on the brake. When reversing it feels like its going to stall out and not quite as bad when accelerating from a stop. Shudder/jumping also happens when going about 50 mph again. The code has popped back up (yet) and no clue what the hell is going on. Please help I am at my wits end on this one!!!

Gotta it all figured out. Somehow the plug wires for 5 & 6 got switched. Kinda feel like an idiot but oh well.