I would delete all partitions on the 1TB drive so you end up with all unallocated space then create a new Primary partition of about 350GB and leave the rest of the drive as unallocated space. This is sometimes refered to as "choking, or short stroking " a drive. It restricts the the system to the fastest part of the drive giving you better performance. Should you get close to using 70% of space on the partition, you can then extend it. I would not however go larger than 500GB.
Below is a how to do a clean install of Window 7. You will know most of the steps but you should consider following the recommendation given in Part 2, Step 14,
This is just a suggestion and up to you, consider doing the following.
When you have installed the OS, updated. Do a custom install from the MB disk, do not install the optional software. then update drivers.
When the desk top is up and running, keep using the windows security options, install Virus protection, install you usual Browser and set to default
Do not install anything else.
Using the windows built in tools, create a drive image and restore disk.
Test the system for stability.
Connect the remaining HDDs, and install other software.