Could be that the EGR is opening as you think. Since it doesn't do it when cold, it's most likely the EGR vacuum regulator solenoid or EGR pressure feedback sensor. The EGR shouldn't open until two conditions are met: 1) The vehicle has warmed up 2) The vehicle is operating at driving speeds as determined by the TPS position. The ECU controls the vacuum regulator based upon coolant temp and TPS position. Check the EGR pressure feedback sensor first, as it's the most likely cause since it doesn't do it until the engine warms up.
You could block the EGR port like you suggested, but you'd probably get poor fuel economy and an EGR associated check engine light error.
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Good Luck...
mj
'01 Ford Ranger 3.0 Super Cab, K&N Air, MaxFlow Exhaust, Oversize Tires 
'93 Ford Taurus 3.0 (Ugh! What a MONEY PIT! Traded it in for the '01 Ranger) 
'87 Ford Ranger 2.3 Super Cab (Owned it for 16 years until some clown t-boned me in it!) 
'92 Ford Aerostar 3.0 (Gave it to Ex in Divorce Settlement) Hehe...
'74 Ford Maverick 250 ci (Great car! 110 mph on Autoban! Traded it in for the '87 Ranger)
'66 Ford Mustang 200 ci (Screwed up and SOLD IT!!)  | 
