With a cowl hood you should probably be fine, I'm running an LS with a truck intake (much taller than LS1 or LS6) and I have a stock hood on a 69 Firebird....but I only have about 3/8 of an inch clearance. If you want I can measure the height of my intake and you could compare it to your holley.
Build looks awesome so far.
-John
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1962 Nova, LS1/ T56, DSE Mini tubs and subframe connectors, Church Boys 4 link, Viking coil overs, C6 brakes
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