I did complete rebuild on the motor about 450 miles ago.  I can ride the bike about 10 miles and it skips the most when running at a steady speed..  Then let it sit for a while and if it skips going back home it is not noticeable.  I have changed plug and the plug cap, I am using the original cap with a new B9es now. Wondering about CDI, what else could it be?

That's conjures up interesting thought of a happy DT360 skipping home. But she isn't happy. So i'm wildly guessing that heading out its all uphill & a fault in the trans gear dogs is showing up & skipping over the dogs. On the way home it's all downhill so the load is 'mostly' off the dogs so doggies don't need to try hard to drive. Hope i'm Very Wrong but that'll start the ball rolling.
Edit to add, are you talking top gear as top [5th] is always bad for rounding of the dog ears & dog slots then slip over when the selector submits to heat of trying to hold it in gear then wears badly & bends away slightly. Early trans were more prone to that & by "74 they'd improved the trans with a total motor revamp. 3rd gear was a bad as well. Ok maybe we're just Brutes down here & hard on trans--clutch [what clutch] never use it after starting off lol.

Ok, part two. Re-think. Is it a bit rich on the slide needle miss firing on the way out, then on the way home it slightly uphill so trying harder & misfire isn't showing up. Maybe lift the clip a notch. Need a bit more info first just to be sure of the symptoms.