What parts of the EGR system can come off?

All of it can be removed -->

You'll need block-off plates for the head and the intake chamber. Be sure to install the appropriate resistor if you haven't already (when you do the normal, BPU EGR-disable mod). If you have the Sound Performance fuel system you will use the fuel pressure guage mount to double as a block-off for the manifold. You COULD remove the EGR passage from inside the manifold, but I think it would be nearly impossible without sawing open the top of the manifold, then re-welding it.

Steve

You can actually use a pipe plug to block off the upper intake. You can do the same on the lower intake, but it won't fit too tight because the hole is a little large.

I'd recommend a plug up top and a plate below.

As far as plate, I believe Mohd's plates are intended to be used 'with' the stock egr parts to give the illusion that the system is still working. I don't think they'd seal well with the stock parts because they are fairly thin.

The other plates seem very pricey but do look nice. If you do the pipe plug up top and a plate below, chances are no one will see the lower plate and it won't matter if they look good anyways. Go to a hardware store and buy some aluminum and make your own if you want to save a LOT of money.