Trying to create a rig from scratch - My mesh "handles" flip and scale I have been creating a rig from scratch because the rigify add-on gives me trouble when I remove parts of the foot. I also wanted to learn to make one myself.

The issue I'm having, is that every time I replace a bone with a mesh I created from a curve, it flips, it scales and changes its location.
I make sure not to make changes to the rig handles unless in Edit Mode.
I have also attempted to adjust the Global position once the replacement bone is set by clicking Ctrl + A (apply then scale and rotation) but often times it only scales it so that it can be big enough to see.
I've also tried to fix the bone itself so that there is no unnecessary rotation.

So I find myself tweaking this for hours and the final rig ends up being imperfect. What are the steps for doing this professionally, please?
Make your mesh &amp; bone structure then do the following:

1st - Download and install "orient_custom_shape_V2.py"
from: https://developer.blender.org/F207430

in Blender at Top:
File > User Preferences > Add-ons > Rigging > check the box for "Rigging 

Orient Custom Shape"

2nd - Import Illustrator splines or draw curves directly in Blender
3rd - Ctrl + j to join all curves in your object (two at a time)
4th - Select objects then Alt + C (convert to mesh)
5th - Set each object to size and position then Select each then Ctrl + A 

to apply roation and scale and location
6th - Name each bone then name each new object you created
7th - Select Armature (bones) then go into "Pose Mode" select a bone then 

in the bone tab on the right scroll down to find "Custom Shape" dialogue 

box &amp; write in the name of object to change for (Remember to click the 

"Wireframe" box just at the left)
8th - Under the "Custom Shape" you'll see "At" box in which you give the 

name of the bone
9th - Finally just click on "Orient Custom Shape"

Now in "Object Mode" you can click on your character mesh, then Shift + 
click your rig