If your state does not do a tailpipe sniffer test, you can add a simple EGR block off plate between the EGR valve and the exhaust feed tube and no one but you will know it is there. Everything from a visual standpoint will look fully in place. Only a tailpipe sniffer test on a dyno would expose the EGR being blanked off. See picture below.
Blanking it off will also let you remove the butterfly plate out of the FCV as well. Only takes a few minutes to remove two small torx screws and it slides out.
If you are not worried about visual inspection, you can remove the complete EGR system and all its components with a kit you can purchase on eBay.
Removing everything will require a reflash of the ECM (engine control computer) to get rid of DTC's (check engine light) that will be set when you unplug the EGR valve and FCV valve. Also a plus, complete EGR removal allows removal and elimination of all the EGR coolant hose connections, a source for coolant leaks.
As to flushing the engine, with the head off I have no idea how this could be accomplished. Normally a complete disassembly of the engine would be required to soak the block and clean out all passageways.
Mountainman or one of the others who have extensive knowledge of the bottom end of this engine may could help guide you in this area?
See Item 9 in picture 2 below.
You could just wait until you get it all back together and use an engine flush additive in the oil running it up to normal temperature and draining the oil doing this several times. But doing it this way you always run the risk of breaking something loose and stopping up something else. It would be a gamble!!!
Piston Cooling Jets no. 9
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Supporting Vendor and Moderator of LOST05 Jeep Liberty CRD Limited
Ironman Springs/Bilstein/Shocks
Yeti StgIV Hot Tune
Week's BatteryTray
No FCV/EGR
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SunCoast/Transgo
Carter Intank-pmp
2mic.Sec.Fuel Filter
Flowmaster/NO CAT
V6Airbox/noVH
GM11 Bld.fan/HDClutch
IronrockArms/wwdieselMount98 Dodge Cummins 24 Valve