well the second 02 sensor further down the exhaust shouldn't matter if it is unplugged, it has no worries on mine
the hardpipe you are talking about on the intake manifold that points down should be going to the egr vsv... is your egr still on there or have you removed it?
it's a good thing you plugged it for now as leaks will create high idles
make sure that your pcv lines aren't blocked causing excessive crankcase pressure
there should be two lines coming off the valve covers, and one off the throttle body venting back into the intake
have you made sure you don't have an oil leak, ensure your oil level is full
the ticking may also be an exhaust leak, next time pop the bonnet and have a listen and see if you can determine which part of the engine it is coming from
and as said previous, don't clear your codes, read them and then get back to us with the codes so we can help you further
