The TRW/Federal Mogul L2316F Forged pistons do come in +0.040. They always have, that's why I would be using them...seem to be the only one. With how much the rest of this engine is going to cost, I'd rather not cheap out on hypereutectic pistons. Its only $150 more anyway.
The 800cfm edelbrock AVS will work fine. Its much more tunable than your average Holley 3310 on the primary side anyway with its replaceable jets, metering rods, & step up springs. I have an Innovate LC-1 wideband and adjusted the crap out of the holley 600 on my 360 and its just not anywhere near a mileage machine....it has never gotten better than 13 mpg.
Also, read this article: http://www.moparmusclemagazine.com/...ocks_thunder_series_avs_carburetor/index.html He has a similar combo and was getting 16.6 MPG. If you know how to tune it, the car does not know the difference between Holley & edelbrock...only that its not choking on lack of CFM and getting the proper A/F mixture.
I wouldn't even attempt running it at under 0.035" clearance. Lots of people running 0.039" (Zero deck+closed chambers+standard gasket).