[scottj]

I wouldn't go any shorter than a 6.25 rod with a 4" stroke and rpm's are why. The 6.25 rod allows for a lighter piston with very little increase in rod weight. Lighter pistons mean less stress at the high piston speeds you see with a 4" stroke. You also reduce friction somewhat. Also, if it is a high-HP motor, the longer rod makes for a smoother power delivery than say a 6" rod which tends to have "snappy" power.
Scott

Edit: In my motor we cut the deck down from 9.5 to 9.3 and used a 1.063 CH piston. We did this because I turn it 8000 rpm (endurance not drag) and light pistons are manditory with a 4" stroke. The pins are in the rings but it causes no problems at all.