Toolbar placement in 9.x Standard within IE8

I'm having a bit of difficulty with the configuration of a 3rd-party Acrobat plugin (msi installation package) and a custom registry value provided by the vendor that enables the enable the 'Comments and Markup' toolbar, for the Acrobat plugin in IE8, and packaging these registry modifications in a GPO that I can deploy throughout my organization. I can reproduce a desired configuration locally on a workstation or terminal server environment consistently, but when a new domain user logs into enviroment, all of these changes are lost.
My goal is to capture the registry entries consistent with a "good" configuration, and deploy these changes via GPO. Using regshot, it seems that there are over 600+ registry changes HKCU in the Adobe and other various shell folders when I'm able to achieve a 'good' configuraion. I'm at a loss at how to capture these changes in a GPO, or if someone at Adobe knows of a simpler way to approach this.
I realize this seems a bit nebulous, so a description of my workflow may help.
Install Acrobat 9.0 standard. Patch all the way up to 9.5.2
Install 3rd-party vendor .msi plugin
Double click vendor provided .reg file that enables the 'Comments and Markup' toolbar. Without this registry file, 'Comments and Markup' toolbar is not a toolbar that can be normally enabled within .pdf's that are opened via IE8.
Arranged toolbars into desired placement - https://www.dropbox.com/s/tj74dcu4b6ls7m1/Screen%20Shot%202012-09-01%20at%2010.54.14%20AM. png
Double click vendor provided .reg file to 'freeze' toolbars into where they were set. This works about 90% of the time. If it doesn't, I re-open a .pdf, rearrange the toolbars, and apply the .reg file again. Hopefully it works, if not, keep restarting and trying until it does. If it is successfull, you only have to set it once.
Again though - you can set these changes for an individual user's domain enviroment, but if a new user logs into the same workstation, you have to redo the entire process over gain. I've been battling this for about six months - I'd like to move our organization over to terminal services/VDI, but the way Windows stores registry information, and how dependent we are on this toolbar, we cannot move forward until we solve this.
Also, would this be an issue that Adobe Professional Services may be able to help me with? I certainly wouldn't mind paying to have someone who has experience in this area and is able to solve this issue for us, assist our organization with this.

Let me restate what I had said previously. It's the location of the toolbars and how the toolbars 'hang' within acrobat that's the problem, not the 3rd party plugin. It needs to be set for every user. For example, in the screenshot I provided - I've customized the 'Comments and Markup' toolbar to have black ink on annotations (default is red), enabled the eraser, and deselected a bunch of shapes that are on by default. I then set it to 'hang' on the left hand side of the screen (see the screenshot in my original post). I also disabled 'tasks' and 'page navigation' toolbars, which gives me enough room to fit both the 3rd party plugin/toolbar and the other non-Comments and Markup toolbars into a horizontal pane.
Also, 'Comments and Markup' does not appear by default. The vendor provided a .reg file to ensure the 'Comments and Markup' toolbar is available to select from the toolbar list. Even though it's available to 'enable', the user needs to manually enable it, and then make the customizations listed above for the correct options/hanging protocol.
Is there a way to automate this?

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