This plan is fine. You've got the main points of re-install, leave the data on the other drive, reconfigure each app to have its data directory on the other drive.
When you install Win7 on the SSD, be sure that non of the HDDs are attached to the system. If you install Win7 while your current boot drive is attached, it will actually leave the boot loader on the HDD and not build one on the SSD.
Rather than putting the SSD in the SATA slot currently occupied by the HDD, I recommend putting it in SATA slot number one. That way, connecting and disconnecting eSATA drives won't screw up your boot order. (of course, if your HDD is now attached to slot 1, that's the same as what you wrote.)