So today I took my upper intake off to clean egr port, also changed spark plugs, adjusted valves, cleaned IAC, cleaned everything I could, replaced gaskets. After all said and done, start it up after a little bit of cranking and has rough idle. Then cel came on with misfire on 4, 5 and 6. Any thoughts? Or good troubleshooting tips or where to start?

Everything worked fine before I did all that. The main reason for doing it was cel was on for egr insufficient flow.

 

Also it's a 2000 EX V6

 

Check idle Long Term Fuel Trim and Short Term Fuel Trim w/ OBD2 scanner. If high LTFT & STFT (> +20% combined) look for a intake air leak on front cylinder head intake. A reduction from idle values of LTFT & STFT at higher rpm (2000-3000) also suggests intake air leak.

good luck