JC,
Sorry about the issues you are running into. I have a few notes:
1) The inability to add / remove software is due to a combination of the fact that you copied the install (yes, same Pulse client Id for several machines where it should be unique) and the fact that the c:\program files\genuitec folder was not copied as well.
2) Installing files into c:\program files\genuitec is something we will fix in our upcoming installer. Even so, there is a way around it now if you perform a single manual step before the install – however, replicating the installed content may cause issues – I will confirm and provide more details later today.
What version of MyEclipse do you currently intend to install and use?
3) We do have an archived update site which can be used to install MyEclipse (you can find it on our download page). This install does not include Pulse though and you will not be able to use any collaborative or sharing features that are provided free for MyEclipse users.