I finished cutting the taller Y plates last night.
It went very well 
Here is the finished plate:
You can see how clean the edge is
Here it is compared to the original plate
One corner had a bit of a problem while cutting the initial pocket outline and I could not figure out why. Later when I was cutting the final profile outline I discovered why.
The Z axis was hitting the clamp! 
As it is I have barely any clearance:
Rather than have a belt slip or miss a step it just powered on through, the gantry flexing a bit, knocking the path of bit off for a moment but not slipping in any way. Once it got past it everything was back in alignment.
Before the upgrade that would have caused lost steps and trashed the print.
So I am very happy with my modifications. 
I also replaced by $5 collet adaptor with an actual 1/8" collet and that seemed to make a big difference as well. (Less runout)
The next step will to be get these installed and setup.
I also want to look into longer Y rails.
I have 2 goals:
Be able to carve on the face of a 2x4 post. These taller brackets should allow that.
Be able to cut on a 2’ x 4’ sheet of material. For larger projects and multiple, smaller objects at a time. Longer y rails should allow that.