I have an '05 GT with 169,000 miles. I went through the injector issue a LONG time back - probably 3 years and 85,000 miles ago. Replaced two injectors with factory replacements from subarupartswarehouse.com, sent those to deatchwerks for rebuilding and have been ready for another to go, but they never have. At ~168,000 miles, the turbo finally went (I know, I am lucky to go that far.) Local ASE mechanics (not dealer - dealer here is not good option) tried to replace the turbo with aftermarket brand to save some $$ and gain some power. Did not go well, that turbo came apart in the first 200 miles. After the repair of the bad replacement turbo, I started getting the rough idle issues like you describe - would often choke out at stop lights, but ran pretty well at higher RPMs. Cleaned MAF, ran the codes and shop said it needed a "tumble generator valve position sensor" - problem is, you cannot buy that sensor, you must buy the intake manifold assembly, which has that sensor pre-installed. If your shop is relating this issue to the intake, it might be this sensor.
I called SOA and complained about requiring people to buy an intake manifold assy just to get a $50 sensor which attaches with two machine screws to the outside of the manifold. No response to date.
By the way, my 2005 with 169,000 miles has ~150 on the compression test.... I think I lucked out with the durability of the powertrain I got on this one...