The first one (red one) goes to your control soleniods mounted aft of the passenger side strut tower brace. Off the top of my head and not looking it up, I believe these soleniods control vacuum to the EGR valve and the smog pump control valve.
The smog pump (air pump) control valve directs air pump air to eithier the heads or the cats.
Just leave it connected to minimise check engine lights, even if you dont have the smog pump installed, or the EGR valve.
I have my EGR valve blocked off internally at the manifold, but the vacuum line is still connected and i leave the red line that you mentioned hooked up as well. The other lines coming from that cluster (which it looks like you have already removed anyway) go to the smog pump. You should block off the open holes in the cluster with RTV to prevent vacuum leaks.
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2002 GT
1993 GT (SOLD)
'93 Mustang GT
RHC member #142
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