I have to honest and tell you, that looks like a hot mess. Not saying that to hurt your feelings; it's just not safe.
Fantastic. No hurt feeling. Just want to get it corrected.
Was your friend a licensed electrician, or just someone that worked for an electrician?
The electrician was a guy that worked with my dad. He no longer works there, so that may be why.
It would've been nice if he'd taken a look at your progress just to check your work. I haven't seen that many code violations at the same time, and all in one panel.

Counted at least 10.
There should be a #6 ground wire pulled with those feeders.
I have a #2 that I can pull.
I'm afraid to ask if those feeders are on a breaker in the main load center? What size?; are they in conduit?
The feeder line is +/-45' #2 going to a 100-amp breaker. They are not in conduit.
What does that 2-pole 60-amp breaker feed?
The 60-amp breaker goes to an HVAC unit. It was installed by the HVAC guy. I guess this is sized right. My other HVAC unit in my Main panel goes to a 40a breaker.
That sub-panel is sized too small for all those breakers; too many piggyback breakers in one panel.
Are the # of breakers a problem or the total load? I added extra breakers so that I could isolate to specific areas. For ex. 1 breaker for wall plugs in garaged, 1 for wall plugs in my shop area, 1 for wall plugs for living room, 1 for wall plugs in bath and bedroom, 1 for lights in garage, 1 for lights in shop.......
Get a tube of this:
http://www.idealindustries.com/products/wire_installation/accessories/noalox.jsp and put it on all the aluminum connections.
(shut off the feed at the main load center first.
Will do.
Was the feed from the main panel sized for copper or aluminum wire?
Aluminum or Copper. Is 45' #2awg on a 100amp breaker within code?
When you separate the ground & neutral buses, it looks like a few of the branch circuits are too short to reach to the other bar.
Can I just leave the existing bus bars like they are and just add a bus bar at the top of the box for the grounds?
Note: Alabama follows the 2008 NEC at the very least.