EGR is easier to remove once the upper intake is off. I recently had to pull my intake to clean up the EGR port, but decided to ditch the non-working EGR and swap a few other things while it's apart. If you are going to remove the EGR, make sure you get rid of the cooler plate on the back of the head, and block the port on the passenger side on the back of the head.
As far as the manifold goes, 5 12mm bolts and 2 12mm nuts. I bypassed the coolant lines as well, using a 3/8" hose barb and clamps and spliced them together. Granted my hoses were still in good shape.
Just take your time and have a little patience. A TSRM is handy but not nescessary. If you don't have one, you can always look here:
http://cygnusx1.net/Supra/techtips.aspx