The Shocking Conclusion
To conclude this thread,
First I'll summarize what has happened up until here. My engine was having intermittent problems and I found a broken cam chain tensioner bolt. I took the engine with me to fix up over winter.
Here is where the story continues. I put the engine back together and slapped it back on the bike. All was running well. I decided to go for a short ride, but while i was on the freeway I suddenly lost power. The reserve switch didnt fix it, so I pulled over to find a big puddle of oil under the engine. Turns out I didn't tighten the drain plug enough and it had come out on me after about ten miles.
After some pushing and some new quarts of oil, the bike was running again, but it would never run the same again. The intermittent running issue got worse, and the engine would sometimes not start altogether.
I thought through the different possible issues and approaches to this more severe problem. After about 4 weeks, I decided to swap out the engine if I could find a good enough deal.
I found a cheap running engine with low miles (about 14,000) on ebay. When it arrived, I swapped out the old engine and now the bike runs great. It has so far shown no signs of the old running issue.
Thank you all for your time and your help. The last few months were quite a journey, and now I can sleep easy knowing that my rebel is running strong. I wish everybody the best of luck with theirs! Safe riding!