Run /boot from one drive and run everything else from another

[BigC]

I have recently installed a new 40gb hard drive and installed windows onto it. I can boot just fine and it runs just fine off of the new OS, but it won't recognise that all my programs are on the original drive. The programs don' run when I select them in program files folder and don't show up in the start menu

 

[Rakk]

I suspect you will probably have to reinstall any of the programs that no longer work, because currently they are probably looking for registry entries (that were created on original installation) which are no longer where there are expected to be, you should be able to install on the now secondary hard drive in the same place as the original though

 

[vanthus]

You will need to reinstall all the programs that are on the second hard drive.
Edit. as Rakk just said.