Why are you making things so complicated?
I uploaded this approach here(pdf):
http://www.ebzw.be/KJFK-VOR13.pdf
If you look in the profile view you will see that the distance from the MAP to THR is 2.6Nm for 13R and 3.6 for 13L
MDA/MDH = 800/787
So for 13L you should descend with 787/3.6=218 ft/Nm, that is 2.2º (1º=100 ft/Nm)
Your rate of descend should be groundspeed in Nm/min times Ft/Nm. Lets so your GS is 120 KTS so 2 Nm/min, therefore your VVI should read 436 Ft/min.
If you insist on a 3º final you should stay level for 1Nm (30 sec in this example) or initially descend at 300 ft/min for example to intercept the 3º glide
13R: 787/2.6=303 ft/Nm (3º)
303x2=606 ft/min
Bart