Well, I finally had an opportunity to continue work on my file server. Haven't had much time with the holidays and having a cold the last two weeks.
I had bought custom braided sata cables when I rebuilt my file server. However, they had two inches of hard shrink wrap on the ends which made the cable stick out too far to fit into my case. The reason I got these was due to the fact that the 90 degree ones were not long enough to connect through the back of the hard drive mounting bracket in my case.
I broke out the heat gun and was able to get some custom bends in the cables. Worked out pretty well. After reconnecting all the drives, I was able to test it out and all of the drives were recognized. Yay!
I was able to get the back side panel on the case. The next part of the project will be to move the file server's UPS under the desk (with the other one) so I can push the larger case back further. It's significantly larger than the previous one.
While I was moving stuff around, I realized that I was not using my KVM switch any longer due to it not supporting the higher resolution of my monitor. So, I took the device and all the cabling out from under my desk. I plan on hooking keyboard and mouse up to the monitor after I run uplink cables from the computers (main rig, file server) to the monitor. But I found out that my cables won't reach the monitor. So, I ordered a six-foot extension for the keyboard and two 9 foot 3.0 ones for the uplink.