John, thank you and very informative explanation. :thumbup:
To make a long story short the main culprit of my problem was low vacuum from the intake that caused a partial closed air valve and thus created the thumping sound from the very beginning.
Since I had the intake manifold gasket and all the hoses under the IM replaced back in June, this car has come alive
Just wanted to say that I'm glad you solved your PITA SAS/SAP problem, Alex.
Just for clarification the SAS system pumps air and hence oxygen directly into the exhaust manifold and exhaust system to help the CATs light off quicker thereby reducing cold start emissions sooner. Since the upstream O2's are in open loop during cold start and warmup, they are used by the ECU to detect a lean mixture which means that the SAS system is working. If the O2's detect a richer mixture, they indicate low or no flow from the SAS and set fault codes accordingly. Once the O2's go into closed loop, the SAP has shut off as has the vacuum to the check valve and the SAS job is done and the upstream O2's go back to their normal job of feeding the ECU info for mixture control.