<font size="6">It works!</font>
OK, after doing an extensive search through the deep dark hidden corners of the internet looking for any type of a hint on how to implement this I came across an email in Adobes email past-bin. Pender said to Adobe that the simplicity of pender is that it gets baked into the project so that the user doesn't have to touch anything but the JavaScript of there own project.
So I used a not so optimized earlier version .capx of my game Falling Fruit Frenzy, exported it from Construct 2 for PhoneGap, zipped it up, named it app.zip, placed it on my C: drive, opened up the pender-android folder, right clicked on the tools folder, opened the Git Bash command prompt, typed ./pendertools -p C:/app.zip, hit enter, and it baked it right into my app.zip folder.
I then made another export from the same .capx, zipped it up and left it as is. Then I ran some tests using PhoneGap Build. Here are the results:
Tested on Samsung Galaxy S3
Without Pender:
Here is a screenshot from my phone. Notice how web font works in the upper left corner. Also notice in the bottom right corner It says 39 fps, with 24 objects on the screen most of them moving at angles.
<img src="http://i46.tinypic.com/14sfll1.png" border="0">
With Pender:
Notice how the web font doesn't work anymore just like CocoonJS. Also notice the increase in fps. 50 fps with 31 moving objects. That's a gain of 19 fps.
<img src="http://i50.tinypic.com/14o0m87.png" border="0">
I bet if you built this in eclipse it would even be faster.
Still though my game using CocoonJS runs 60, to 62 fps on the same phone so IMO Cocoon is still superior.
I would like to see what other peoples games are getting for performance with Pender. Please give it a try and post your experiences here.