I didn't ride her around last night because it was getting dark and didn't know want to risk it. It appears it's settled down A LOT-

Rode around the block and it died on me a couple times. Once I let off the throttle it was rough (chugging back and forth) and took some time to realize I had pulled back on the throttle again.

Decided to keep riding since it progressively smoothed out after riding a few miles. After five or so miles it was acting as though nothing was wrong! It idled, it responded to changes in throttle instantly, and there was nothing that felt out of place!

That burning smell was present, but I may have figured that problem out. I noticed a pool of fork oil on the wheel after I parked it. The smell was definitely there once I put the sidestand down, but went away after a few minutes. I noticed fork oil on the right side (throttle side) of the engine and the front wheel fairing.

Here's where I'm at now:
1) It runs perfectly after being warmed up- I'm waiting for the engine to cool down to see if things will be different.

2) What does burning fork oil smell like? I'm guessing it smells bad.

3) There still seems to be a bit of play in the throttle cable. Could this be linked to an idle issue? Or should I disregard this?
***
Forgot to mention that I felt the voltage regulator and along some of the wiring. The VR felt barely warm after a 30-40 minute ride and I couldn't feel any warm/hot spots along any of the wiring.
***
Smell
That smell only comes around when there's fork oil on the engine. If the bike sits still and idles, there's no smell.

Throttle Cable
Now, I know there's supposed to be some play in the throttle cable, but I just felt like there was some "extra" play in the throttle cable. More than what was there before. I'm probably just nitpicking at everything after all that's been going on with this bike.

Charging
I plan on testing the charging system as soon as I'm able to. At this moment I'm just making a checklist of everything I need to do, once I get some free time.

Battery
Now, I put in a different (old) battery into the bike. The old battery is what got the bike running, and is what I currently have in it. I tried starting with the new (HD) battery in, but all that came of it was that machine gun click. I'm thinking the battery isn't as good as it was when Harley load tested it. For now, though, I'm keeping the old battery in there.

Mileage
I'm slowly putting miles on it, but the weather isn't allowing me to put on as many as I would like! I rode to my university yesterday and clocked about 30 miles. Thirteen to 15 miles in to the trip is when everything started to smooth out.

Lights
I read some people have done a modification where both headlights are turned on when the high-beam is turned on. With this modification, the low-beam gets moved to the accessories circuit/accessories fuse. When I turn on the high-beam, both headlights come on, so I'm guessing this is what was done to the wiring harness before I got it.