Yes you will have to reinstall your programs and drivers
which could be a huge job. Nowadays, installing windoze, its updates, and a load of apps can easily take 2 days. I have done it many times. Built a new PC week ago, at the office; took a few days to get everything from the old one transferred and working (using a 128GB SSD, BTW, lightning fast).
as per #7 I have a SATA already installed but running as storage only. Will this affect the drivers I need or does installing the drivers from the mobo CD to get the storage SATA to work do the lot?
I saw that, but I don't know. I think it depends on the motherboard SATA controller. ISTM that when one first connects a SATA drive, the SATA controller presents it as an IDE drive, which windoze can access using its built-in drivers (which is why there is never any F6+diskette business if installing windoze on an IDE drive). This is how windoze initially starts up when you are doing a fresh install, and it may be how it may be accessing a second (non-boot) drive. But really I could be wrong.
What kind of BIOS settings do you see for the SATA controller? If you see something like "compatibility mode" (which I get on my Thinkpad, for example) that will probably be an IDE-lookalike mode.
If you look at Properties and Driver for the SATA HD, what driver do you see there? Is it the M$ one, or is it the SATA controller vendor's one? Having said that, I have just looked at the Driver for the a.m. SATA SSD (which is definitely running via a 3rd party SATA driver) and it shows a 2001 M$ driver....
Edit: the other day I cloned an IDE drive to a SATA one (purely to speed up one old and awfully slow machine) with the latter on an Adaptec SATA/PCI controller. Prior to doing this, I installed the Adaptec drivers (off their CD) on the windoze installation. Then I closed the HD with Trueimage, pulled out the old HD, set the BIOS to boot off the SATA controller, and off it went.