Rough idle sounds like a vacuum leak after the MAF. Do you have a way to do a boost leak test? I would venture to guess that there is poor sealing or bad intake manifold gasket.
The tick could be an injector (already a maybe), valvetrain (probably not) and exhaust leak. Don't forget to check the EGR air valves, if loose or not sealing, you will get a terrible exhaust leak and valve tick. A bad enough exhaust leak will give false readings to the o2's and cause a rough idle as well (rich fuel mixture). What do the o2's say at idle?