To tell the truth, i have nerer tried to estimate rye yield, but i am going to give it a try this year. From what i have gathered so far you first have to figure how many heads in a square foot of area. If they are planted in rows, divide 144 square inches by your row width in inches to get the lenght of row in inches for a square foot. In our case the rye was planted in 7.5 inch rows so 144/7.5= 19.2 inches of row = 1 square foot.
 Then count the heads in 19.2 inches of row and multiply the average seeds per head by the number of heads, and multiply that by 43560 (sq ft in a acre) to get the number of seeds/acre.
Then divide that by what you think the kernal wt is (seeds per lb.)  i am going to use 19000 seeds per lb. that will give you lbs of grain per acre, then divide that by 56 to get the bu./acre estimated yield.
 So how did you sow the rye was it in rows, or was it broadcast?
 Hope this helps, but if it is clear as mud i am willing to explain it better if i can.