Well, unless you've got a JDM ecu or standalone engine management hardware you'll want to replace the EGR system... dumb to pull it in the first place thinking it'll somehow improve performance. Can't say about the vacuum surge, but it was there for a reason and it's not expensive so I'd plan on replacing it as well. Someone with more knowledge of the alarm system will have to chime in on checking it out.
Fair warning, a lot of owners start ripping, removing, and generally screwing up their Supras with their "repairs" and "modifications", usually with adverse consequences. You may have a hard time putting that one back in running order,
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