Not sure about the intake question, but you should leave the filter housing in place. It protects the filter from the warmer engine bay air. You can take the air silencer off, though.
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"Back in the day"-Red '66 289
"Later"- Black '68 289
"Today"- White 2000 GT
Stock except K&N & Flowmasters
ET-13.952@98.87 RT-.507 60'-2.09
Son #1 - '87 GT stock
Son #2 - '89 LX 5.0 stock