Oh.... just noticed you're in Cali.... you'll have 2 oxygen sensors, 2 cats, 2 EGR VSVs and an EGR temp sensor to inspect on top of the AFM and EGR valve. First and foremost make sure the plumbing from the valve to the intake is clean then check for error codes in the ECU.
http://www.cygnusx1.net/Supra/Librar...Section=EX&P=2
Check: Dashpot, EGR,
http://www.cygnusx1.net/Supra/Librar....aspx?S=EC&P=1
Check air flow meter, EGR gas temp sensor, oxygen sensor and sub-oxygen sensor:
http://www.cygnusx1.net/Supra/Librar...ction=FI&P=118
Yes, you can remove most of the EGR components with the engine still in th car; The cooler plate is a MAJOR pain though and unless it's leaking it probably doesn't need to be removed. Just test it as shown above and clean out the plumbing for it. It's not the cause of high HC; It's the cause for most high NOx numbers (which you also failed on).
This covers all the likely suspects.
Is there much oil coming through your PCV system into the intake?