I have been researching the same issue and have found that it really isn't a problem.
I spoke with the Tech guys at Holley. Their mounts, headers and 302-2 oil pan were designed to work fine with the factory AC evap housing.
Here is a thread detailing a swap using G8 exhaust manifolds and the factory AC evap housing. The mounts he used required cutting the trans tunnel to use a 6L80e transmission, so the Holley mounts may be a better route to take, however, I have read details on another swap that used the Holley mounts and f-body exhaust manifolds and they fit with the evap housing.
As information for anyone who comes across this thread that is looking for this information, every component in the new Hooker 1st-gen F-body LS swap system is compatible for bolt-in installation with the factory A/C or SB or BB heater cores. That includes the long-tube headers, mid-length headers and the Hooker LS swap cast iron exhaust manifolds when these items are installed on an engine that was mounted with the Hooker 12618HKR engine bracket kit and one of the Hooker transmission crossmembers.
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