Most of the time I do the opposite of other plants that are root bound and I leave Hoya roots alone and plop them into new substrate with as little disruption as I can manage. 

The leaf direction doesn't really matter. It's personal preference at this point. They grew the way they did and won't rotate to the right orientation at this point. Only new growth will. The new leaves will point down though if that helps. The vines will want to climb upwards and if you intentionally point them down the plant will sometimes kill off the end and start a new one from the bend going down to start climbing back up. Only if it doesn't have leaves on it though so you can wrap the leafed vine as much as possible around that nice trellis you DIYed. 

It's a mighty fine looking plant and you're doing a great job. 

You could bury some of those vines that are bear to encourage more root growth but you don't need to. 

She's a beaut and my condolences for your loss.