I will go ahead and post my success story for anyone interested in the future.
As stated above, I was able to generate a hex file from 4 commands listed above and only my source file (.c in this case), and .sopcinfo file. I was concerned about this hex files functionality because it was different from what the make targets option gave me in the GUI. I ended up including this new hex file in my project and it worked as expected!
One thing I would like to note.
When using make targets in the GUI, you are given a hex file along with a meminit.qip. This .qip is to be added to your quartus project in order for the tools to find the proper initialization files. In my case, using the command line method did not produce this .qip file. I ended up including the .hex file in the project and the Nios "found it" no problem. I am guessing that the "include memory initialization file" option for the Nios memory in Qsys allowed for no need of the meminit.qip.
Hope this helps.
Matt