Told me to come get it and pick up my check. He just couldn't fix it!
What does he mean by "pick up my check'? He didn't charge you for any of the work?
Sounds like a poor choice from the start, in hindsight.
So you jumped it and it ran fine? Makes it sound like just the battery is bad. A car will usually run OK after being jumpstarted, and continue running fine, assuming the alternator is working, so I'd discount the "alternator not connected properly thery. I'd get the battery charged and tested and go from there.