Start by seeing if any codes are pending in OBDII. If it's running that bad some should be pending even though no CEL.
Otherwise, it's pretty much anyone's guess and you could spend a lot of time and $ chasing unnecessary parts...
Could be MAF (which you can try cleaning or disconnecting/running in safe mode), might be a coil pack (6k should have shaken any bad install out before now but look at them to see if any might be cracked), maybe AOS starting to fail but usually it'll just go w/ lots of smoke (pull off j-tube at TB and look for any oil pooling), vacuum leak big enough would trigger CEL before rough running would be noticed.
Good luck
