Make sure the inline filters are removed from the turbo oil feed and AVCS solenoids (if it has them). They are little filters like in the tip of an injector inlet, tucked in the banjo bolts of the turbo oil feed and whenre the oil lines go into the AVCS solenoids on the top of the heads right by the intake cam gears. This is a recall item for all 04-07 Scoobs, so don't be surprised if there are none.
Most/all of the 2.5 ECUs have a misfire/roughness monitor. Pick up a cheap Tactrix 1.3U cable (should be nice and dirty cheap as the 2.0 is $160-170 new) and scan it with RomRaider. 1-3 counts is nothing, and in fact there should be none, but if you ever see one cyl piling up count it probably has a broken ring land. The nice thing about a Tactrix cable on a Scoob is you can disable emissions CELs and force all the readiness monitors to pass, if you live in a scantool emissions area.
Get rid of the EGT probe pre-turbo ASAP. All they do is break off and cash turbos. Replace the probe with a 2.2K ohm resistor. Be prepared to replace your catted uppipe, or at least hollow it out at some point; typical break free/turn sideways/bad shit happens.
Exhaust rattles or exhaust hitting the frame = stimulates the KS = you'd think the car is fucked and coming apart.
Uhm, there's 1001 little tips and tricks to those cars... all pretty simple to figure out, to be honest. They are odd cars, but not hard.