Hyundai Repair: hesitation on acceleration, platinum plugs, quality wires

Question
Just a day or so ago, I replaced the input speed sensor in my 2001 santa fe. All the problems I was having with that seem to be corrected. It seems to be shifting fine, no longer being put in 3rd gear. Now, when I step on the gas it wants to hesitate and jump a little before it starts taking off. It started this while I was having the stuck in 3rd problem, so I assumed they were related. One time yesterday while stopped my rps jumped a little and i felt the car shudder, but that happened just once. We had this same problem a couple years ago except it was a little worse and it was bad spark plugs and wires. Could this be the same problem, or since the speed sensor was just replaced could it be something with that. My check engine light is still on, but it has been on because I got te EGR system code last time and I have yet to get that taken care of. Should I reset the codes and wait for the light to come back on and get them read again? FYI I have 108K miles and i think spark plugs and wires were replaced around 60-70K.  

Answer
It's possible that your EGR valve is sticking open, causing this issue.  Your engine won't run properly at idle or low RPM if the EGR valve is open.

It could also be an issue with your spark plugs or wires.  If you didn't use platinum plugs, or used low quality wires, it's probably about time to replace them again.

I'd recommend starting with clearing the trouble codes if you haven't already done so since replacing the transmission input speed sensor.  Then, when the check engine lamp comes back on, check to see what codes are present.  

If at any time your check engine lamp flashes, you have a significant misfire that could cause comverter damage.  In that case you should stop driving the vehicle until the misfire is repaired.  In most cases, misfires are caused by plugs, wires, or coils.