Hey Joe.
Im familiar with your issues. Ive experienced the bogging when my son first began riding the 65, as if the bike is still cold or "loaded up" but have obviously warmed up the bike and like you said revs fine on the stand. I feel like I could hop on the bike and take off just fine as an experienced rider knowing when to throttle up and maybe work it through the "bog" if you know what I mean. I will agree that it may be a learning curve with the transition to clutch life..
Here's what I've come up with. If your plug fouls the bike will not run. Or will sound very unhealthy when revving if it is running, but will eventually die. I've got an '18 yz65 for my son and have had a plug foul. What fuel ratio are you running,and what jet set up? I've had a good relationship with Pax Racing throughout our 50cc career lol and talked to them about jetting and fuel ratio. 135/50 and 40:1 is their advice. I know this has helped us out, and the bike is ripping great and no more problems