Federal dam measurments are from the lowest to the highest points in a dam. In reading throught he link you gave, I would feel pretty confident in saying that IN requires the measurement to be from the ORIGINAL elevation of the stream bed under the center of the dam to be where either the max water level is or the top of the dam.

Again your local NRCS agent can answer these questions and pu the regs in laymans terms.

If you are under the 20 foot threshold and your water shed is way below the sq mile threshold and 2.5 ac is not going to be near 100 acre feet of volume, you have no permit issue or requirement.