I'm having a hard time looking up BPT, could you tell me what it stands for?
As for the EGR lines, when removing the EGR pipe from the exhaust and intake manifolds, there are still
a bunch of vacuum lines and a solenoid left over (along with a temperature probe). It's possible to remove the main EGR pipe (goes from exhaust manifold to intake manifold) without causing any vacuum leaks or problems as long as you plug up both holes properly. I believe it's also possible to remove some additional parts of the EGR system and cause a vacuum leak.
Your problem sounds more like an idle adjustment issue, but since it happened after you removed the EGR valve that is likely the cause. Tell me, did you remove the valve from the intake manifold and plug the hole left behind with something? A block-off plate perhaps? Also, did you plug up the hole in the exhaust manifold too? Just to get the obvious out of the way....