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Yes, definitely specify which harness you have. I'm 95% sure the pinout between the gen 2 JDM and the 93-95 USDM are the same. In that case, you would use the 1121 box (AEM EMS) or the JDM jumper config (Nemesis) when you order it.
You will get plug and play for the Nemesis. For speed-density (which you want, that AFM runs out at 250-ish rwhp), you will need to wire in a MAP and IAT sensor set to the AEM EMS.
EGR = Exhaust Gas Recirculation. It's a pollution device that reduces NOx. Japan and most of Europe have very relaxed laws concerning NOx, so Toyota didn't need an EGR for those markets. They had to put it on for the US markets to reduce NOx, as the US is more strict concerning NOx emissions.
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