The article in the link below specifies that 0.015” and greater mismatch of the rails requires machining of the intake-to-head surface of the intake. It doesn’t address machining the bottom of the intake, but keep in mind this may be required also to keep the intake-to-block mating from holding the intake off of the heads . Take a look at the picture that precedes this one also for more intake installation tips.
http://www.carcraft.com/techarticles.../photo_16.html
Steve Christ’s “How to Rebuild Big Block Ford Engines” specifies that if the block-to-head mating surface of either the block or heads have been machined more than 0.020”, the intake will require machining on the head
and block mating surfaces (pg. 101), and has a table for how much to remove from each manifold surface based on head or block machining (pg. 102). If you don’t already have this book, it is well worth it just for the wealth of information on the FE engine, even for someone never planning on rebuilding their own (Book ISBN: 0895860708).