1998 Toyota Corolla engine vibration.

My 98 corolla has started vibrating while idling after warmup. It seems to have worsened since I replaced the plugs and wires. Got noticably worse after replacing the air filter. Doesn't affect permormance, but is very annoying at traffic stops and seems to be vibrating something just behind the speedometer b/c I hear a "thumping" there along with the vibration. It's worse in gear, putting in park or neutral, it smooths out a bit and the thumping goes away. I thought maybe the valve clearance needed adjusted? I hear slight valve tapping, but it's very faint, would it be very loud if it needed adjusted? The engine barely made any noise at all before I replaced the plugs. Though I did not use those factory double pronged plugs it recommended, I just used regular platinums. I'm concerned with the valve tapping and vibration since engine could barely be heard running a few thousand miles ago. Possibly EGR valve? PCV? Check engine light is on. Several codes. There was a vaccuum leak. Any suggestions?