I think you are seeing more than there is to it. I have done that type installation a few times. For your convenience, let me just repeat the few simple steps:
1. Backup all your user data - which you have apparently already done. It is also useful to make a list of all the programs you have installed so that you remember them. And make sure you save the product keys for any purchased programs. You will need those when you reinstall those programs. I would also download the installation .iso of your AV program of choice - e.g. MSE and save it on the backup disk.
2. Install the SSD
3. Unplug the HDD with the current OS. It is easy to check whether you got the right disk - just shut down the PC and then power it up again. If you current OS does not boot, then you unplugged the right HDD. It is not really neccessary to unplug the other HDD also. Also unplug all USB attached devices and the ethernet/internet cable.
4. Shut off the PC again, throw the Win7 installation disk into the optical reader (which is usually the first boot device - if not, you have to set the boot sequence in the BIOS accordingly), shut the bay and switch power on. It should now start the installation process. Select the SSD as disk to where you want to install. It should take about 20 to 30 minutes to install the whole OS. When it gets to the point where you are asked to activate Win7, defer that because you still have the other Win7 installed. Work it to completion of the installation.
5. Power off the PC - then power on again and go into the BIOS setup. Keep tapping the corresponding Function key - the BIOS splash screen will say which is which. Set the SSD as second boot device (after the optical reader which I would always keep as first boot device). Then load your new Win7.
6. Install the AV program from your saved .iso as first step.
7. Get your user files from the backup into the respective new Win7 folders. Should there be any problems, you can also access your user files on your old HDD installation from your new Win7. Just go to Computer > double click on the HDD win7 > users > your name > and voila, there they are
8. Once you are satisfied that your user files are in good order, you can reformat the HDD partition that contains your old Win7
9. Plug everything back in - USB devices, ethernet cable. Now you will be blessed with driver installations and a lot of updates.
10. Now you can activate your new SSD win7 -
http://www.sevenforums.com/tutorials/3408-activate-windows-7-online.html
11. Install all your other programs - I usually do that on an "as needed" basis. Then it is not so much work at one time.
Have fun.
PS: If you print this little guideline, then you can follow it and don't have to remember all that stuff.