I do not know what target audience your software is aimed at, but as I mentioned before, most corporates will be keeping their versions of Adobe Reader bang up to date due to the continuous stream of software vulnerabilities that are being discovered. In addition, the standard Adobe Reader install in machines sold to end-users has the auto-update flag turned on, so pretty much all end users are likely to have versions of Adobe Reader that update regularly.
Frankly, as you have already noted, locking an application to a particular version of Adobe Reader is fatally stupid, as no corporate will adopt a fixed version due to risk from undiscovered vulnerabilities, and end users will be unaware of what is going on most of the time.
Does your installer check for a pre-existing install of Adobe Reader, and what version it is? Do you have a process to uninstall the old version, reboot the machine, then continue with your installation? Unless you are running the very latest release of Adobe Reader (V9.3?) then in many cases, you are going to need to downgrade the customer version to an earlier release, and this WILL NOT be popular. A reboot will also be necessary. As far as I can recall, there is no option in Adobe Tuner to configure the Reader install to downgrade existing versions, so it will be entirely up to you to do it.
You don't mention which operating system you are testing on, but if your intention is to deploy to Vista or Windows 7, you will need to test carefully on both 32 bit and 64 bit editions, as the admin users no longer have admin rights by default, and therefore an installation will request elevation of rights at the beginning of the install, to allow changes to be made to restricted areas such as the Program Files folder (normally read-only )
I would NOT put temporary installation files such as CIC.EXE in the Program Files folder. Since it looks like CIC.EXE is not required after installation, why not just run it from the same source location as your Adobe MSI or EXE is running from? If you must install it somewhere, what is wrong with the TEMP folder?
Is there a reason why your separate file must be deployed after the Adobe and CIC stuff?
Would it not make sense to include it in the Adobe package with Tuner?
As your developers have clearly not given any thought to the issues that will emerge with users upgrading Adobe Reader, they really need to go back to the drawing board and find a more viable solution. One solution that you may wish to consider is to use the Symantec Workspace Virtualisation client and create your install as a virtual application. That way it should be able to co-exist with other versions of Adobe already on the target machine, and the whole install could be pre-prepared by you and shipped as a virtual app.