EGR removal
 

I was doing some research on some exhaust manifolds and when I came across the one that Begi makes I noticed that you could pick EGR or no EGR? If I was to remove my egr before I got a megasquirt would there be side effects? Would it affect my idle? From my understanding when exhaust gases reach a certain temp the egr valve opens and pulls air from the exhaust manifold and sends it through the intake manifold and so on. Correct me if I am wrong. If I was to take this off would my ecu attempt to guess the air/fuel ratio? If it is expecting that extra air to be coming through the egr valve and it is not getting that air would it be adding extra fuel?

you should just wait until you have megasquirt.

It is not difficult.
Install Megasquirt, remove EGR, order turbo kit. In that order.