You have two options with the coolant lines, you can cap them off or connect them... I guess connecting them keeps the coolant flowing though that backside of the intake... it's probably best to connect them.. plus it's a ***** to get to that back side of the intake. Easiest to connect them 
-as
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'89 GT Convertible:
TFS TW Heads, TFS Street Intake, TFS Stage 1 Cam, FMS 1.6 RRs, 24# Injectors, Pro-M 75mm MAF, No Name CAI, 3.73s, O/R H-Pipe, FlowMasters, AOD w/ Trans-Go Shift Kit
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