Engine 67 timing and carb question: 289 2 barrel, stock with stock cast iron intake

Is it possible to set the timing at 6 degrees and not have the rotor pointing to #1 cylinder. I changed the intake gasket, followed every step by the original Ford Shop manual. It runs like it's out of time by one notch. Also my other question is which way does the carb spacer face ? Is the smoothe side up or the chambered side face up? I can't rember how it came off, I installed it with the chamber side up. It ran great before I installed the intake gaskets.
 
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