2004 infiniti i35- engine pulsates while idling

I am hearing/ feeling the engine pulsating (thud) while idling or when stopped at a light. There are no DTS codes. This occured almost immediately after I cleared earlier Code P0305.
I didnt notice any issues till i got check engine light. The code was P0305 indicating misfiring cylinder 5 which is located on the fire wall side under the lower air intake collector. After very tedious (hrs) removal of both lower and upper collectors I accessed the ign. Coils and the spark plugs. I replaced all the spark plugs (too much gap) and packed everthing back and took out for some spin. I noticed this pulsating sound while idling (feels the engine is going to stall) as described. After the long spin the CEL went away but this engine noise continues. Eric can you please guide me what to look for and where?
BTW I have old codes P1614-NATS malfunction, & P1800- VIAS control solenoid. These did not cause the service engine light. Could these faults have any thing to do with engine thudding?
Help me please!!!! Bought this used car recently!