Well, You didn't say if you have the KB throttle cable of not.- You will need that. It's the throttle cable that came with the KB kit originally. BELIEVE me there is a difference between a stock 96-98 Cobra throttle cable and a KB throttle cable.
If you eliminate the EGR you can use that port for the vaccum brake booster.
Also there should be a vaccum port AFTER the blower, located at the front left corner. That port is where you get the boost reference from for your fuel pressure regulator, Bypass valve, and boost gauge.
The three ports BEFORE the blower AFTER the throttle body you can use for anything that need to ONLY see vaccum. Like your, PCV, HVAC vaccum line, ect.
Also a tip that is not in the KB book is this....
As many of you know the KB kit is NOT INTERCOOLED. What you can do to keep your tune safe is tap the intake (near the boost reference port) for your IAT sensor. That way your IAT sensor is reading the Intake air temp AFTER the blower. That way your tuner can setup your IAT timing tables correctly. That way if you come across a hot day your Timing will adjust accordingly.