Short answer: reforge

Long answer: (the bold part is probably what you are missing)
character -->
ninja tool page -->
click on a tool (that you wish to "put" the stat of the essence on) -->
click "ninja tools" *on on the left side (the one next to five natures, where you usually use to upgrade tool level)
click "reforge ninja tools" sub-tab on the top (it's right under "character" actually)
slot essence to the right side of two box
Select the stat you wish to replace on the left (include empty stats) and the right(only one)
fill the bottom as much as you can to increase success
click reforge


do note that reforge might not be unlocked at the level the rest of the ninja tool system is, so the *on might not be there. I'm not sure since I was high enough level when it was released.

Given how rare red gourd is, this isn't strictly true.
I've been collecting the highest crit/atk/nin since 2.0 came out, and I only ever had 4 of them above 75, 2 of which I gave up so I c*e the atk/nin on it instead(I really dont like how you can only pick one...) So if nothing else, the 75 crit essence(which have a bug....) is fairly good.
I do have 10 >=60 nin, but I am also a bit short on atk, only 7 of those.

So while it IS below the maximal stat you can get on gold tools and more so compared to red gourd, they aren't *, sub-optimal but not *.

Ah yes, the current tool stat are indeed *, I've yet to see an attack value over 50... I plan to compile some data to disprove some notions too.... this will be "fun"