Stock 400 SBC rods are 5.56" long. I do recall seeing a crank for the 5.56" rods but I don't recall who made it and I wouldn't recommend using the 400 rods anyway.
As for clearance, rods #2 and #6 are most likely to hit the cam but all of them need to be checked for clearance. You probably will not have any real clearance probs. between the crank and block at 3.75" stroke. Just check to see that you have 0.040"-0.060" clearance between the pan rails and bottoms of the bores and the reciprocating assembly.