Photoshop & NEF
The D90 was first compatible with ACR 4.6, which is the last version that was released for Photoshop CS3. I don't recall if there were problems with that release. But according to the compatibility list provided by Adobe, Photoshop CS3 should open your raw images if you have Camera Raw 4.6 installed. In Photoshop, if you click Help/About Plug-Ins/Camera Raw it should tell you what version you have installed. There should only be one instance displayed. If you were editing raw files with Photoshop CS2, then you must have installed and used the DNG converter to do so.
It might be a good idea for you to reinstall ACR 4.6 and see if that will help you resolve your problem. I'm not sure what you are thinking you are gaining by keeping Photoshop CS2 installed. I cannot cite exactly, but I have read in the past that installing ACR versions for different versions of Photoshop can sometimes get things confused. You would probably help resolve some of these problems by removing Photoshop CS2, but that is a decision you will have to make.
Since you indicated that (if I understand correctly) Photoshop has stopped allowing you to open your NEF files, that would indicate that something has changed that possibly affected your installed ACR. When things have you done to your computer besides install Lightroom 4? Lightroom does not use the ACR plug-in, so that installation should not have caused any problem. So what else have you done that I could have caused this?