I could use some advice for this situation. Last month I purchased a new 2017 model year Honda Africa, 0 miles, 2 year warranty. When I was purchasing the bike, the dealership wanted to know when I was picking up the bike because it was still in the original crate/container it came in and still needed to be opened / put together.

Recently I haven't been able to get the bike to start, I assumed that the cold weather and the battery were the culprit so I purchased a battery tender and a charging harness.

After removing the covering to access the battery, I was very upset/disappointed. I was expecting to find a socket bolt retaining the ground wire to the engine. Instead I found an incorrectly sized hex bolt I could pull out by hand instead of loosening/unscrewing it. The bolt hole threading in the engine looks to be stripped. Worse yet, there are two 1/8" deep drill holes around it that I can't even tell what happened. It almost looks like a drunken attempt to drill out and retap the bolt hole.

I would assume the bike required a battery to be installed among other things if the bike was just opened from its packaging, but I can't imagine how someone could mess up this so badly.

I live in another state about 2.5 hours away from the dealership I purchased the bike from. I emailed the salesman and general email of the dealership I purchased the bike from explaining what I have found and to call me asap. I plan on taking the bike to a local dealership I trust tomorrow to have it evaluated for repair costs and any other "installation errors". I'm worried that the dealership I purchased from is going to say that I caused this damage.

I could use any advice you guys could recommend. Has anything similar happened to anyone else? Any other damage I should check for?

Speak to the manager.
Not service, nobody,,
Manager..
If you're not satisfied
Next stop
Owner..

Take pictures before it leaves your possession and goes to any dealer for repairs. Documentation of everything is paramount, phone calls, names and positions, e-mails, dates, everything concerning the bike repair and dealer response needs to be recorded.
 Don't let them blame the problem on "somebody else" and blow you off. I would already start contacting Honda USA about the problem, just send them a few pictures and a quick explanation of what you found when checking the bike. Include your expectations about either getting it fixed for free or having the entire bike replaced. Make sure the dealer gets the same pictures and text.
 Be nice but firm to start with and don't go medieval on them yet, you will have plenty of time to freak out on them if things go sour. Don't make any threats unless it's about getting a lawyer.
 

The dealer that did it may not have any idea what happened........only the one mechanic may have screwed up and was not willing to man up and tell anybody.

I would take the bike back to the dealer you bought it.....and see what they have to say about it.  If they are a good dealer, they will make it right.